Novel genetic loci associated with disease resistance in soybeans

ABSTRACT

The present invention relates to methods and compositions for identifying, selecting and/or producing a Disease resistant soybean plant or germplasm using markers, genes and chromosomal intervals derived from Glycine tomentella P1441001, P1441008, P1446958, P1509501, P1583970, or P1483224. A soybean plant or germplasm that has been identified, selected and/or produced by any of the methods of the present invention is also provided. Disease resistant soybean seeds, plants and germplasms are also provided.

RELATED APPLICATIONS

This Application claims the benefit of U.S. Provisional Application No. 62/347,945, filed 9 Jun. 2016, the contents of which are incorporated herein by reference.

STATEMENT REGARDING ELECTRONIC FILING OF A SEQUENCE LISTING

A Sequence Listing in ASCII text format, is submitted, entitled 81045 SEQ LIST_ST25.txt and 6.90MB in size, generated on June 9, 2017 and an electronic sequence listing is filed in conjunction with this application. This Sequence Listing is hereby incorporated by reference into the specification for its disclosures.

FIELD OF THE INVENTION

The present invention relates to compositions and methods for identifying, selecting and producing enhanced disease and/or pathogen resistant soybean plants.

BACKGROUND

Plant pathogens are known to cause considerable damage to important crops, resulting in significant agricultural losses with widespread consequences for both the food supply and other industries that rely on plant materials. As such, there is a long felt need to reduce the incidence and/or impact of agricultural pathogens on crop production.

Several pathogens have been associated with damage to soybeans, which individually and collectively have the potential to cause significant yield losses in the United States and throughout the world. Exemplary pathogens include, but are not limited to fungi (e.g., genus Phytophthora and Asian Soybean rust Phakopsora pahyrhizi), nematodes (e.g., genus Meloidogyne, particularly, Meloidogyne javanica), and soybean stem canker. Given the significant threat to global food supplies that these pathogens present as well as the time and expense associated with treating soybean crops to prevent yield loss, new methods for producing pathogen resistant soybean cultivars are needed. What is needed is novel resistance genes (herein, “R-Genes”) that can be introduced into commercial soybean plants to control soybean pathogens

SUMMARY OF THE INVENTION

This summary lists several embodiments of the presently disclosed subject matter, and in many cases lists variations and permutations of these embodiments.

Thus, it is an object of the presently disclosed subject matter to provide methods for conveying pathogen resistance into non-resistant soybean germplasm or plant lines. Further the presently disclosed subject matter provides novel Glycine max lines comprising in its genome a chromosome interval, loci, and/or gene that is derived from Glycine tomentella and further confers Asian soybean rust resistance (herein, ‘ASR’) in said novel Glycine max line.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING

SEQ ID NOs: 1 & 2 are chromosomal intervals derived from Glycine tomentella line accession PI441001 referred to herein as “Scaffold 46840” and “Scaffold 49652” respectively. Scaffold 49652 has been mapped to G. tomentella chromosome 5 and Scaffold 46840 has been mapped to G. tomentella chromosome 5. SEQ ID NO. 3 is a chromosomal interval derived from Glycine tomentella line accession PI 483224 referred to herein as “Scaffold 002687F”. Scaffold 002687F has been mapped to G. tomentella chromosome 5. SEQ ID NO. 4 is a chromosomal interval derived from Glycine tomentella line accession PI 583970 referred to herein as “Scaffold 001084F”. Scaffold 001084F has been mapped to G. tomentella chromosome 5. SEQ ID NO: 5 is a chromosomal interval derived from Glycine tomentella line accession PI583970 herein referred to “Scaffold 000819F”. Scaffold 000819F has been mapped to G. tomentella chromosome 5. Genetic population mapping studies for PI441001, PI483224 and PI 583970 indicate that Glycine tomentella Chromosome 5 contains chromosomal intervals highly associated with ASR resistance (e.g. as corresponding to SEQ ID NOs: 1-5). Tentative data, not to be limited by theory, also indicates that Glycine tomentella accessions PI446958 and/or PI483224 can be used as a source for said chromosomal intervals corresponding to SEQ ID NOs 1-5. These chromosomal intervals or portions thereof may be introduced (i.e. introgressed through use of embryo rescue & marker assisted breeding (MAB)) into Glycine max lines to create Glycine max lines resistant to various diseases such as ASR. Tables 1-5 indicate single nucleotide polymorphisms (SNP) within SEQ ID NOs 1-5 that are associated with ASR resistance. Table 1 displays SNP associations for SEQ ID NO: 1 (Scaffold 46840) and Table 2 displays SNP associations for SEQ ID NO: 2 (Scaffold 49652). Table 3 displays SNP associations for SEQ ID NO: 3 (Scaffold 002687F). Table 4 displays SNP association for SEQ ID NO. 4 (Scaffold 001084F). Table 5 displays SNP associations for SEQ ID NO: 5 (Scaffold 000819F). All alleles for the SNPs identified in Tables 1 -5 were determined to be significantly linked with resistance or susceptibility (p<0.05) to ASR.

TABLE 1 SNP Positions within SEQ ID NO: 1 that are associated with increased resistance to ASR Favorable Unfavorable Allele Allele (Rust (Rust SNP Name Position Resistant) Susceptible) scaffold46840_1828_SNP 1828 T C scaffold46840_3854_SNP 3854 A T scaffold46840_4596_SNP 4596 G C scaffold46840_7871_SNP 7871 G T scaffold46840_16578_SNP 16578 A C scaffold46840_19339_SNP 19339 T A scaffold46840_19702_SNP 19702 C T scaffold46840_19733_SNP 19733 A G scaffold46840_21388_SNP 21388 G T scaffold46840_21389_SNP 21389 G A scaffold46840_21402_SNP 21402 A G scaffold46840_21518_SNP 21518 A G scaffold46840_21519_SNP 21519 A T scaffold46840_23199_SNP 23199 T C scaffold46840_27734_SNP 27734 A C scaffold46840_28944_SNP 28944 C A scaffold46840_31424_SNP 31424 A G scaffold46840_33107_SNP 33107 G A scaffold46840_34009_SNP 34009 C T scaffold46840_53166_SNP 53166 C T scaffold46840_53469_SNP 53469 C T scaffold46840_53908_SNP 53908 A C scaffold46840_54203_SNP 54203 T C scaffold46840_56034_SNP 56034 T G scaffold46840_88414_SNP 88414 G T scaffold46840_98917_SNP 98917 T G scaffold46840_104913_SNP 104913 C G scaffold46840_106826_SNP 106826 T C scaffold46840_106962_SNP 106962 A T scaffold46840_107712_SNP 107712 T A scaffold46840_133407_SNP 133407 T C scaffold46840_135237_SNP 135237 A T scaffold46840_138711_SNP 138711 C T scaffold46840_143396_SNP 143396 G A scaffold46840_143399_SNP 143399 T C scaffold46840_144469_SNP 144469 A G scaffold46840_155153_SNP 155153 T C scaffold46840_156265_SNP 156265 C T scaffold46840_156445_SNP 156445 G A scaffold46840_157487_SNP 157487 A G scaffold46840_160570_SNP 160570 A G scaffold46840_173047_SNP 173047 C T scaffold46840_173086_SNP 173086 C T scaffold46840_175324_SNP 175324 T C scaffold46840_176807_SNP 176807 A T scaffold46840_183058_SNP 183058 G A scaffold46840_185660_SNP 185660 T A scaffold46840_187500_SNP 187500 A G scaffold46840_189638_SNP 189638 G A scaffold46840_193666_SNP 193666 A G scaffold46840_194620_SNP 194620 G A scaffold46840_195623_SNP 195623 A G scaffold46840_199643_SNP 199643 C A scaffold46840_203247_SNP 203247 T C scaffold46840_204613_SNP 204613 A G scaffold46840_205887_SNP 205887 C T scaffold46840_206645_SNP 206645 T C scaffold46840_206670_SNP 206670 A T scaffold46840_207999_SNP 207999 A G scaffold46840_208069_SNP 208069 T G scaffold46840_210361_SNP 210361 G C scaffold46840_210610_SNP 210610 T C scaffold46840_211145_SNP 211145 A C scaffold46840_213594_SNP 213594 A G scaffold46840_213644_SNP 213644 G A scaffold46840_228760_SNP 228760 T G scaffold46840_232915_SNP 232915 G T scaffold46840_244091_SNP 244091 T A scaffold46840_247995_SNP 247995 C T scaffold46840_252031_SNP 252031 A G scaffold46840_252294_SNP 252294 G A scaffold46840_265245_SNP 265245 C G scaffold46840_266739_SNP 266739 G T scaffold46840_292109_SNP 292109 C T scaffold46840_301218_SNP 301218 T A scaffold46840_305019_SNP 305019 A G scaffold46840_305252_SNP 305252 A G scaffold46840_306327_SNP 306327 T C scaffold46840_306369_SNP 306369 C T scaffold46840_308096_SNP 308096 T C scaffold46840_309679_SNP 309679 A T scaffold46840_310247_SNP 310247 C A scaffold46840_310792_SNP 310792 A T scaffold46840_312460_SNP 312460 C A scaffold46840_313406_SNP 313406 A C scaffold46840_329689_SNP 329689 G A scaffold46840_330435_SNP 330435 G C scaffold46840_331328_SNP 331328 G A scaffold46840_337919_SNP 337919 C A scaffold46840_350957_SNP 350957 A T scaffold46840_354267_SNP 354267 A G scaffold46840_355661_SNP 355661 T C scaffold46840_356478_SNP 356478 T C scaffold46840_358994_SNP 358994 T C scaffold46840_363408_SNP 363408 A G scaffold46840_367504_SNP 367504 G C scaffold46840_368441_SNP 368441 A T scaffold46840_371665_SNP 371665 C T scaffold46840_372390_SNP 372390 C A scaffold46840_372415_SNP 372415 T A scaffold46840_380899_SNP 380899 C T scaffold46840_381701_SNP 381701 T G scaffold46840_382539_SNP 382539 A G scaffold46840_384909_SNP 384909 A T scaffold46840_386383_SNP 386383 G A scaffold46840_386883_SNP 386883 G C scaffold46840_387699_SNP 387699 A G scaffold46840_388192_SNP 388192 C G scaffold46840_401306_SNP 401306 G C scaffold46840_402205_SNP 402205 C T scaffold46840_419063_SNP 419063 A C scaffold46840_419121_SNP 419121 C T scaffold46840_419259_SNP 419259 G A scaffold46840_420963_SNP 420963 C G scaffold46840_421037_SNP 421037 C T scaffold46840_421906_SNP 421906 T C scaffold46840_424476_SNP 424476 C T scaffold46840_426504_SNP 426504 T C scaffold46840_426550_SNP 426550 C T scaffold46840_433738_SNP 433738 C A scaffold46840_435442_SNP 435442 C T scaffold46840_435446_SNP 435446 T C scaffold46840_435456_SNP 435456 G A scaffold46840_436445_SNP 436445 G T scaffold46840_436844_SNP 436844 T G scaffold46840_437526_SNP 437526 G T scaffold46840_438692_SNP 438692 C A scaffold46840_440329_SNP 440329 G A scaffold46840_441638_SNP 441638 T C scaffold46840_442882_SNP 442882 C T scaffold46840_444624_SNP 444624 C T scaffold46840_444829_SNP 444829 G T scaffold46840_444833_SNP 444833 C T scaffold46840_445506_SNP 445506 T C scaffold46840_451845_SNP 451845 A G scaffold46840_455083_SNP 455083 G A scaffold46840_455349_SNP 455349 G C scaffold46840_456838_SNP 456838 C T scaffold46840_456840_SNP 456840 C T scaffold46840_456888_SNP 456888 G A scaffold46840_457510_SNP 457510 G A scaffold46840_459924_SNP 459924 A T scaffold46840_493769_SNP 493769 G A scaffold46840_493863_SNP 493863 T C scaffold46840_495644_SNP 495644 G A scaffold46840_498269_SNP 498269 G C scaffold46840_500187_SNP 500187 C T scaffold46840_524750_SNP 524750 G A scaffold46840_531774_SNP 531774 G C scaffold46840_532217_SNP 532217 A G scaffold46840_532460_SNP 532460 C A scaffold46840_532849_SNP 532849 C T scaffold46840_533165_SNP 533165 T G scaffold46840_534674_SNP 534674 A G scaffold46840_534815_SNP 534815 T C scaffold46840_541100_SNP 541100 T C scaffold46840_547800_SNP 547800 A G scaffold46840_548096_SNP 548096 A T scaffold46840_548651_SNP 548651 A G scaffold46840_548909_SNP 548909 C A scaffold46840_550359_SNP 550359 A G scaffold46840_554136_SNP 554136 T C scaffold46840_557231_SNP 557231 G C scaffold46840_557476_SNP 557476 T C scaffold46840_559239_SNP 559239 G T scaffold46840_566877_SNP 566877 G T scaffold46840_573263_SNP 573263 C G scaffold46840_576344_SNP 576344 G A scaffold46840_576937_SNP 576937 T A scaffold46840_581793_SNP 581793 T C scaffold46840_631321_SNP 631321 T A scaffold46840_632437_SNP 632437 T C scaffold46840_644135_SNP 644135 G A scaffold46840_646516_SNP 646516 A C scaffold46840_646661_SNP 646661 C T scaffold46840_650395_SNP 650395 C G scaffold46840_650533_SNP 650533 T G scaffold46840_650883_SNP 650883 T C scaffold46840_680820_SNP 680820 T C scaffold46840_700296_SNP 700296 G T scaffold46840_709091_SNP 709091 T C scaffold46840_717250_SNP 717250 A G scaffold46840_717919_SNP 717919 C T scaffold46840_723204_SNP 723204 A G scaffold46840_737847_SNP 737847 A C scaffold46840_742854_SNP 742854 G C scaffold46840_761047_SNP 761047 C T scaffold46840_763626_SNP 763626 G A scaffold46840_767022_SNP 767022 A T scaffold46840_773124_SNP 773124 G A scaffold46840_795852_SNP 795852 G A scaffold46840_844662_SNP 844662 A T scaffold46840_856241_SNP 856241 C T scaffold46840_864819_SNP 864819 A C scaffold46840_868404_SNP 868404 T A scaffold46840_881483_SNP 881483 G A scaffold46840_881687_SNP 881687 G A scaffold46840_948734_SNP 948734 C G scaffold46840_951580_SNP 951580 C A scaffold46840_979277_SNP 979277 C A scaffold46840_984144_SNP 984144 A G scaffold46840_985119_SNP 985119 A G scaffold46840_990969_SNP 990969 T G scaffold46840_991246_SNP 991246 G A scaffold46840_996069_SNP 996069 A T scaffold46840_996617_SNP 996617 T C scaffold46840_1005071_SNP 1005071 G T scaffold46840_1012711_SNP 1012711 C A scaffold46840_1013144_SNP 1013144 A T scaffold46840_1013502_SNP 1013502 C T scaffold46840_1013853_SNP 1013853 G T scaffold46840_1014491_SNP 1014491 A G scaffold46840_1017387_SNP 1017387 T G scaffold46840_1017454_SNP 1017454 C T scaffold46840_1017456_SNP 1017456 A G scaffold46840_1017513_SNP 1017513 G A scaffold46840_1017562_SNP 1017562 G A scaffold46840_1017580_SNP 1017580 A G scaffold46840_1018041_SNP 1018041 G C scaffold46840_1018803_SNP 1018803 A G scaffold46840_1018807_SNP 1018807 A T scaffold46840_1018808_SNP 1018808 A T scaffold46840_1018809_SNP 1018809 A T scaffold46840_1019830_SNP 1019830 T A scaffold46840_1019879_SNP 1019879 C T scaffold46840_1023021_SNP 1023021 A G scaffold46840_1025444_SNP 1025444 T C scaffold46840_1027183_SNP 1027183 T C scaffold46840_1027185_SNP 1027185 T C scaffold46840_1027206_SNP 1027206 C T scaffold46840_1028386_SNP 1028386 T A scaffold46840_1035663_SNP 1035663 T G scaffold46840_1050796_SNP 1050796 A T scaffold46840_1092407_SNP 1092407 C T scaffold46840_1092836_SNP 1092836 A T scaffold46840_1097462_SNP 1097462 G T scaffold46840_1100700_SNP 1100700 C A scaffold46840_1107270_SNP 1107270 C G scaffold46840_1108688_SNP 1108688 T C scaffold46840_1110411_SNP 1110411 G A scaffold46840_1110578_SNP 1110578 G A scaffold46840_1113083_SNP 1113083 C A scaffold46840_1128638_SNP 1128638 A G scaffold46840_1132152_SNP 1132152 A T scaffold46840_1145964_SNP 1145964 T G scaffold46840_1151108_SNP 1151108 T C scaffold46840_1152027_SNP 1152027 T C scaffold46840_1164739_SNP 1164739 A C scaffold46840_1179177_SNP 1179177 A G scaffold46840_1196044_SNP 1196044 T C scaffold46840_1208547_SNP 1208547 T A scaffold46840_1222050_SNP 1222050 T C scaffold46840_1236321_SNP 1236321 C A scaffold46840_1238462_SNP 1238462 A T scaffold46840_1245039_SNP 1245039 A T

TABLE 2 SNP Positions within SEQ ID NO: 2 that are associated with increased resistance to ASR Favorable Unfavorable Allele Allele (Rust (Rust SNP Name Position Resistant) Susceptible) scaffold49652_5217_SNP 5217 T C scaffold49652_17452_SNP 17452 T C scaffold49652_17508_SNP 17508 T C scaffold49652_18133_SNP 18133 G A scaffold49652_23299_SNP 23299 T G scaffold49652_23932_SNP 23932 T A scaffold49652_25316_SNP 25316 C T scaffold49652_27493_SNP 27493 C T scaffold49652_31604_SNP 31604 A C scaffold49652_33717_SNP 33717 T C scaffold49652_33754_SNP 33754 G A scaffold49652_33815_SNP 33815 C T scaffold49652_35579_SNP 35579 A G scaffold49652_42441_SNP 42441 C T scaffold49652_45742_SNP 45742 A G scaffold49652_47403_SNP 47403 G T scaffold49652_50271_SNP 50271 C G scaffold49652_50273_SNP 50273 A C scaffold49652_52163_SNP 52163 A G scaffold49652_53843_SNP 53843 T C scaffold49652_53867_SNP 53867 T C scaffold49652_57089_SNP 57089 A G scaffold49652_60723_SNP 60723 C T scaffold49652_62132_SNP 62132 T C scaffold49652_64164_SNP 64164 T A scaffold49652_65402_SNP 65402 G A scaffold49652_67001_SNP 67001 G T scaffold49652_68551_SNP 68551 G A scaffold49652_88556_SNP 88556 A G scaffold49652_90063_SNP 90063 T C scaffold49652_95177_SNP 95177 A G scaffold49652_95604_SNP 95604 C T scaffold49652_98488_SNP 98488 G A scaffold49652_112122_SNP 112122 G T scaffold49652_119068_SNP 119068 T C scaffold49652_129424_SNP 129424 G A scaffold49652_130808_SNP 130808 A G scaffold49652_136261_SNP 136261 C A scaffold49652_159300_SNP 159300 G T scaffold49652_164108_SNP 164108 G A scaffold49652_164267_SNP 164267 C T scaffold49652_164427_SNP 164427 A G scaffold49652_176366_SNP 176366 T A scaffold49652_178148_SNP 178148 T C scaffold49652_181207_SNP 181207 T C scaffold49652_182444_SNP 182444 A G scaffold49652_183913_SNP 183913 G A scaffold49652_185602_SNP 185602 A C scaffold49652_193012_SNP 193012 A G scaffold49652_196752_SNP 196752 T C scaffold49652_197492_SNP 197492 G A scaffold49652_197499_SNP 197499 T C scaffold49652_197616_SNP 197616 G A scaffold49652_199871_SNP 199871 G A scaffold49652_200228_SNP 200228 A G scaffold49652_203298_SNP 203298 G A scaffold49652_205904_SNP 205904 G T scaffold49652_206666_SNP 206666 A G scaffold49652_208874_SNP 208874 C T scaffold49652_215183_SNP 215183 G A scaffold49652_215265_SNP 215265 A G scaffold49652_216104_SNP 216104 G A scaffold49652_217181_SNP 217181 C T scaffold49652_218571_SNP 218571 A G scaffold49652_219511_SNP 219511 T C scaffold49652_219529_SNP 219529 A G scaffold49652_219575_SNP 219575 C T scaffold49652_219952_SNP 219952 G A scaffold49652_219953_SNP 219953 G A scaffold49652_219963_SNP 219963 T C scaffold49652_220068_SNP 220068 C A scaffold49652_220176_SNP 220176 G T scaffold49652_221463_SNP 221463 C A scaffold49652_222090_SNP 222090 G A scaffold49652_222099_SNP 222099 A G scaffold49652_222102_SNP 222102 A G scaffold49652_222109_SNP 222109 G A scaffold49652_222189_SNP 222189 G A scaffold49652_222205_SNP 222205 C A scaffold49652_222306_SNP 222306 C T scaffold49652_222440_SNP 222440 T A scaffold49652_222903_SNP 222903 C A scaffold49652_222937_SNP 222937 T C scaffold49652_222944_SNP 222944 G A scaffold49652_223876_SNP 223876 C G scaffold49652_223933_SNP 223933 C G scaffold49652_224422_SNP 224422 C T scaffold49652_225283_SNP 225283 G C scaffold49652_225922_SNP 225922 T C scaffold49652_226654_SNP 226654 G C scaffold49652_227737_SNP 227737 T C scaffold49652_228474_SNP 228474 A G scaffold49652_229075_SNP 229075 A G scaffold49652_230244_SNP 230244 T C scaffold49652_230528_SNP 230528 G T scaffold49652_238854_SNP 238854 C G scaffold49652_240022_SNP 240022 C T scaffold49652_240304_SNP 240304 C T scaffold49652_250663_SNP 250663 G A scaffold49652_251169_SNP 251169 A G scaffold49652_251304_SNP 251304 A G scaffold49652_252410_SNP 252410 T C scaffold49652_266259_SNP 266259 G A scaffold49652_269948_SNP 269948 G A scaffold49652_276433_SNP 276433 A G scaffold49652_279239_SNP 279239 T A scaffold49652_287492_SNP 287492 C A scaffold49652_287493_SNP 287493 A C scaffold49652_287554_SNP 287554 A C scaffold49652_289763_SNP 289763 A T scaffold49652_291185_SNP 291185 G T scaffold49652_291711_SNP 291711 C T scaffold49652_293833_SNP 293833 T C scaffold49652_293985_SNP 293985 A G scaffold49652_294334_SNP 294334 A T scaffold49652_294339_SNP 294339 T G scaffold49652_294569_SNP 294569 A C scaffold49652_294571_SNP 294571 T A scaffold49652_294582_SNP 294582 A G scaffold49652_296085_SNP 296085 A T scaffold49652_297573_SNP 297573 A T scaffold49652_297580_SNP 297580 T C scaffold49652_297847_SNP 297847 A C scaffold49652_298949_SNP 298949 A C scaffold49652_299350_SNP 299350 G C scaffold49652_300420_SNP 300420 G C scaffold49652_300424_SNP 300424 A G scaffold49652_301124_SNP 301124 G A scaffold49652_301167_SNP 301167 T A scaffold49652_301238_SNP 301238 T A scaffold49652_301913_SNP 301913 T C scaffold49652_302027_SNP 302027 A C scaffold49652_302168_SNP 302168 G C scaffold49652_302219_SNP 302219 T C scaffold49652_302434_SNP 302434 G T scaffold49652_302450_SNP 302450 T A scaffold49652_302683_SNP 302683 G T scaffold49652_303688_SNP 303688 T C scaffold49652_303860_SNP 303860 C A scaffold49652_304361_SNP 304361 G A scaffold49652_304888_SNP 304888 A G scaffold49652_304894_SNP 304894 A G scaffold49652_304927_SNP 304927 C T scaffold49652_304978_SNP 304978 T C scaffold49652_305002_SNP 305002 C T scaffold49652_305014_SNP 305014 T A scaffold49652_305380_SNP 305380 T C scaffold49652_306466_SNP 306466 C G scaffold49652_306538_SNP 306538 A C scaffold49652_308411_SNP 308411 C G scaffold49652_308438_SNP 308438 C A scaffold49652_308835_SNP 308835 C T scaffold49652_308836_SNP 308836 A G scaffold49652_308930_SNP 308930 T C scaffold49652_309042_SNP 309042 A G scaffold49652_309062_SNP 309062 A C scaffold49652_309971_SNP 309971 A C scaffold49652_310193_SNP 310193 A C scaffold49652_310385_SNP 310385 T A scaffold49652_310406_SNP 310406 T G scaffold49652_311266_SNP 311266 C A scaffold49652_311330_SNP 311330 T C scaffold49652_311522_SNP 311522 T C scaffold49652_311789_SNP 311789 A G scaffold49652_311935_SNP 311935 G A scaffold49652_311938_SNP 311938 T C scaffold49652_312257_SNP 312257 G A scaffold49652_312289_SNP 312289 T C scaffold49652_313499_SNP 313499 C G scaffold49652_313588_SNP 313588 C T scaffold49652_314672_SNP 314672 A G scaffold49652_315497_SNP 315497 A G scaffold49652_315498_SNP 315498 A G scaffold49652_315527_SNP 315527 G A scaffold49652_316007_SNP 316007 G T scaffold49652_316309_SNP 316309 G A scaffold49652_316425_SNP 316425 T G scaffold49652_317362_SNP 317362 C G scaffold49652_318444_SNP 318444 A T scaffold49652_318600_SNP 318600 G T scaffold49652_318645_SNP 318645 C T scaffold49652_318669_SNP 318669 T C scaffold49652_318696_SNP 318696 C G scaffold49652_319094_SNP 319094 T C scaffold49652_319397_SNP 319397 C A scaffold49652_319704_SNP 319704 G A scaffold49652_320373_SNP 320373 A G scaffold49652_321853_SNP 321853 T A scaffold49652_325751_SNP 325751 T A scaffold49652_326774_SNP 326774 G C scaffold49652_327926_SNP 327926 A C scaffold49652_327964_SNP 327964 G T scaffold49652_328344_SNP 328344 C T scaffold49652_328346_SNP 328346 T G scaffold49652_328748_SNP 328748 G A scaffold49652_329021_SNP 329021 T G scaffold49652_329291_SNP 329291 G T scaffold49652_329315_SNP 329315 A C scaffold49652_329561_SNP 329561 G A scaffold49652_329660_SNP 329660 A T scaffold49652_329903_SNP 329903 G C scaffold49652_330206_SNP 330206 C T scaffold49652_330224_SNP 330224 A T scaffold49652_330593_SNP 330593 A G scaffold49652_331196_SNP 331196 T C scaffold49652_333099_SNP 333099 G A scaffold49652_333133_SNP 333133 T C scaffold49652_333359_SNP 333359 T G scaffold49652_333413_SNP 333413 C T scaffold49652_333453_SNP 333453 G C scaffold49652_334022_SNP 334022 C A scaffold49652_334587_SNP 334587 T C scaffold49652_335926_SNP 335926 T C scaffold49652_336373_SNP 336373 C T scaffold49652_336392_SNP 336392 T C scaffold49652_336422_SNP 336422 G C scaffold49652_336783_SNP 336783 C G scaffold49652_336839_SNP 336839 G T scaffold49652_337703_SNP 337703 A G scaffold49652_337918_SNP 337918 A G scaffold49652_338070_SNP 338070 T G scaffold49652_339859_SNP 339859 C T scaffold49652_340107_SNP 340107 A G scaffold49652_340120_SNP 340120 G C scaffold49652_340174_SNP 340174 C T scaffold49652_341049_SNP 341049 G T scaffold49652_341264_SNP 341264 C A scaffold49652_345335_SNP 345335 A G scaffold49652_345365_SNP 345365 A T scaffold49652_345374_SNP 345374 A G scaffold49652_345484_SNP 345484 C T scaffold49652_345554_SNP 345554 G A scaffold49652_345575_SNP 345575 T C scaffold49652_345600_SNP 345600 A C scaffold49652_347890_SNP 347890 A T scaffold49652_347970_SNP 347970 T G scaffold49652_347974_SNP 347974 G A scaffold49652_347979_SNP 347979 G A scaffold49652_347996_SNP 347996 G T scaffold49652_349930_SNP 349930 C T scaffold49652_349948_SNP 349948 T G scaffold49652_351367_SNP 351367 T A scaffold49652_351556_SNP 351556 T C scaffold49652_351856_SNP 351856 G A scaffold49652_352037_SNP 352037 G A scaffold49652_353477_SNP 353477 C T scaffold49652_353505_SNP 353505 G A scaffold49652_354088_SNP 354088 T C scaffold49652_354298_SNP 354298 A C scaffold49652_354374_SNP 354374 C T scaffold49652_355975_SNP 355975 G T scaffold49652_356979_SNP 356979 G A scaffold49652_358191_SNP 358191 A G scaffold49652_360296_SNP 360296 T C scaffold49652_360986_SNP 360986 C A scaffold49652_362062_SNP 362062 G A scaffold49652_365432_SNP 365432 A G scaffold49652_366972_SNP 366972 C T scaffold49652_367235_SNP 367235 C T scaffold49652_374498_SNP 374498 C A scaffold49652_376756_SNP 376756 T G scaffold49652_381774_SNP 381774 G C scaffold49652_400199_SNP 400199 A G scaffold49652_400786_SNP 400786 C T scaffold49652_402643_SNP 402643 T A scaffold49652_403055_SNP 403055 A T scaffold49652_403379_SNP 403379 C T scaffold49652_403705_SNP 403705 C T scaffold49652_404201_SNP 404201 G A scaffold49652_404905_SNP 404905 G C scaffold49652_409753_SNP 409753 C A scaffold49652_411457_SNP 411457 A C scaffold49652_414901_SNP 414901 C G scaffold49652_416379_SNP 416379 G A scaffold49652_418210_SNP 418210 A G scaffold49652_433538_SNP 433538 C T scaffold49652_440036_SNP 440036 T C scaffold49652_449338_SNP 449338 A T scaffold49652_449339_SNP 449339 A T scaffold49652_453711_SNP 453711 G A scaffold49652_458506_SNP 458506 A G scaffold49652_467749_SNP 467749 A T scaffold49652_468384_SNP 468384 C T scaffold49652_474262_SNP 474262 G A scaffold49652_481700_SNP 481700 T A scaffold49652_481980_SNP 481980 A G scaffold49652_482017_SNP 482017 T A scaffold49652_482729_SNP 482729 C A scaffold49652_483114_SNP 483114 T C scaffold49652_483134_SNP 483134 A T scaffold49652_483238_SNP 483238 C G scaffold49652_483844_SNP 483844 T C scaffold49652_488135_SNP 488135 T C scaffold49652_489130_SNP 489130 C A scaffold49652_489402_SNP 489402 A G scaffold49652_490245_SNP 490245 G A scaffold49652_490567_SNP 490567 C G scaffold49652_490679_SNP 490679 A G scaffold49652_490686_SNP 490686 G A scaffold49652_490712_SNP 490712 A G scaffold49652_499896_SNP 499896 C A scaffold49652_500864_SNP 500864 G A scaffold49652_503510_SNP 503510 G C scaffold49652_504360_SNP 504360 A G scaffold49652_505008_SNP 505008 C T scaffold49652_505051_SNP 505051 A T scaffold49652_510409_SNP 510409 T A scaffold49652_519990_SNP 519990 C A scaffold49652_523968_SNP 523968 T C scaffold49652_531222_SNP 531222 A G scaffold49652_540357_SNP 540357 T A scaffold49652_551070_SNP 551070 G A scaffold49652_559257_SNP 559257 C T scaffold49652_559979_SNP 559979 A G scaffold49652_561291_SNP 561291 A G scaffold49652_567130_SNP 567130 A T scaffold49652_570015_SNP 570015 G A scaffold49652_570373_SNP 570373 C A scaffold49652_582494_SNP 582494 A T scaffold49652_586011_SNP 586011 T A scaffold49652_586012_SNP 586012 T A scaffold49652_591947_SNP 591947 G A scaffold49652_592239_SNP 592239 A T scaffold49652_594778_SNP 594778 T G scaffold49652_596868_SNP 596868 G T scaffold49652_599890_SNP 599890 T C scaffold49652_602894_SNP 602894 C T scaffold49652_608314_SNP 608314 A T scaffold49652_608649_SNP 608649 A G scaffold49652_609274_SNP 609274 C G scaffold49652_610620_SNP 610620 A G scaffold49652_610745_SNP 610745 G A scaffold49652_610785_SNP 610785 C T scaffold49652_610978_SNP 610978 A G scaffold49652_611812_SNP 611812 G C scaffold49652_612916_SNP 612916 A T scaffold49652_615662_SNP 615662 G T scaffold49652_615802_SNP 615802 T A scaffold49652_616179_SNP 616179 G A scaffold49652_619723_SNP 619723 A G scaffold49652_623226_SNP 623226 T C scaffold49652_623262_SNP 623262 G A scaffold49652_623316_SNP 623316 T G scaffold49652_623971_SNP 623971 A G scaffold49652_625797_SNP 625797 A T scaffold49652_626033_SNP 626033 C G scaffold49652_626576_SNP 626576 C T scaffold49652_636530_SNP 636530 T C scaffold49652_636591_SNP 636591 G A scaffold49652_640814_SNP 640814 T A scaffold49652_641023_SNP 641023 A G scaffold49652_642961_SNP 642961 C G scaffold49652_645742_SNP 645742 T A scaffold49652_649825_SNP 649825 G A scaffold49652_650622_SNP 650622 T A scaffold49652_650911_SNP 650911 G A scaffold49652_652582_SNP 652582 A G scaffold49652_653269_SNP 653269 A T scaffold49652_655875_SNP 655875 T G scaffold49652_655945_SNP 655945 A G scaffold49652_657235_SNP 657235 G A scaffold49652_657572_SNP 657572 C T scaffold49652_657890_SNP 657890 A G scaffold49652_660730_SNP 660730 A T scaffold49652_661085_SNP 661085 A G scaffold49652_661178_SNP 661178 A T scaffold49652_664050_SNP 664050 C A scaffold49652_671483_SNP 671483 A G scaffold49652_672897_SNP 672897 G A scaffold49652_675995_SNP 675995 A G scaffold49652_677013_SNP 677013 T C scaffold49652_677538_SNP 677538 C T scaffold49652_677686_SNP 677686 T G scaffold49652_677824_SNP 677824 G A scaffold49652_678252_SNP 678252 T C scaffold49652_678661_SNP 678661 G A scaffold49652_680010_SNP 680010 G T scaffold49652_680049_SNP 680049 C A scaffold49652_680102_SNP 680102 T C scaffold49652_681611_SNP 681611 C T scaffold49652_681834_SNP 681834 T C scaffold49652_683219_SNP 683219 A C scaffold49652_683499_SNP 683499 A G scaffold49652_685162_SNP 685162 A T scaffold49652_686427_SNP 686427 C T scaffold49652_686466_SNP 686466 G A scaffold49652_686575_SNP 686575 G A scaffold49652_690420_SNP 690420 G A scaffold49652_691001_SNP 691001 C T scaffold49652_691511_SNP 691511 G A scaffold49652_691562_SNP 691562 G A scaffold49652_694449_SNP 694449 T G scaffold49652_698078_SNP 698078 C T scaffold49652_698468_SNP 698468 C T scaffold49652_699891_SNP 699891 T A scaffold49652_701425_SNP 701425 C T scaffold49652_701847_SNP 701847 G A scaffold49652_702517_SNP 702517 T G scaffold49652_703686_SNP 703686 C A scaffold49652_704754_SNP 704754 T A scaffold49652_704765_SNP 704765 G T scaffold49652_707130_SNP 707130 C A scaffold49652_707457_SNP 707457 C T scaffold49652_708022_SNP 708022 C T scaffold49652_708235_SNP 708235 C T scaffold49652_711647_SNP 711647 C G scaffold49652_712665_SNP 712665 A G scaffold49652_718466_SNP 718466 T G scaffold49652_721386_SNP 721386 G T scaffold49652_722079_SNP 722079 G A scaffold49652_722931_SNP 722931 T A scaffold49652_724109_SNP 724109 C A scaffold49652_728106_SNP 728106 C T scaffold49652_729138_SNP 729138 A T scaffold49652_729202_SNP 729202 A G scaffold49652_731436_SNP 731436 C G scaffold49652_731484_SNP 731484 T A scaffold49652_731952_SNP 731952 C T scaffold49652_731997_SNP 731997 G A scaffold49652_732184_SNP 732184 C T scaffold49652_732236_SNP 732236 G A scaffold49652_732255_SNP 732255 T C scaffold49652_732256_SNP 732256 C T scaffold49652_732274_SNP 732274 A G scaffold49652_732285_SNP 732285 C T scaffold49652_732447_SNP 732447 T C scaffold49652_732546_SNP 732546 G A scaffold49652_732958_SNP 732958 T C scaffold49652_733147_SNP 733147 A G scaffold49652_733195_SNP 733195 C A scaffold49652_733199_SNP 733199 A G scaffold49652_733207_SNP 733207 A G scaffold49652_733321_SNP 733321 T C scaffold49652_733978_SNP 733978 A G scaffold49652_734856_SNP 734856 G T scaffold49652_735577_SNP 735577 C T scaffold49652_736430_SNP 736430 A G scaffold49652_737005_SNP 737005 C T scaffold49652_737576_SNP 737576 C G scaffold49652_740567_SNP 740567 C T scaffold49652_743622_SNP 743622 C T scaffold49652_748166_SNP 748166 T A scaffold49652_748594_SNP 748594 C T scaffold49652_762558_SNP 762558 T C scaffold49652_763277_SNP 763277 A G scaffold49652_767299_SNP 767299 G T scaffold49652_769480_SNP 769480 C T scaffold49652_769644_SNP 769644 A G scaffold49652_778065_SNP 778065 A G scaffold49652_780345_SNP 780345 T A scaffold49652_782788_SNP 782788 C T scaffold49652_783110_SNP 783110 C T scaffold49652_783990_SNP 783990 C T scaffold49652_787357_SNP 787357 T C scaffold49652_787629_SNP 787629 A G scaffold49652_790141_SNP 790141 G A scaffold49652_794383_SNP 794383 A C scaffold49652_794508_SNP 794508 G A scaffold49652_796408_SNP 796408 A T scaffold49652_796483_SNP 796483 C T scaffold49652_797153_SNP 797153 T C scaffold49652_797737_SNP 797737 A T scaffold49652_798218_SNP 798218 G T scaffold49652_798222_SNP 798222 T A scaffold49652_798260_SNP 798260 T A scaffold49652_800544_SNP 800544 T C scaffold49652_804203_SNP 804203 G A scaffold49652_805118_SNP 805118 T C scaffold49652_805150_SNP 805150 A G scaffold49652_805244_SNP 805244 G A scaffold49652_805264_SNP 805264 T C scaffold49652_805452_SNP 805452 T C scaffold49652_805642_SNP 805642 G A scaffold49652_805649_SNP 805649 G A scaffold49652_805890_SNP 805890 T G scaffold49652_807572_SNP 807572 C T scaffold49652_807576_SNP 807576 G T scaffold49652_808401_SNP 808401 A T scaffold49652_809462_SNP 809462 T C scaffold49652_817467_SNP 817467 A G scaffold49652_818447_SNP 818447 G A scaffold49652_818500_SNP 818500 G A scaffold49652_820447_SNP 820447 G A scaffold49652_821025_SNP 821025 T C scaffold49652_821660_SNP 821660 T C scaffold49652_821725_SNP 821725 C T scaffold49652_821732_SNP 821732 T C scaffold49652_821777_SNP 821777 A G scaffold49652_821778_SNP 821778 G A scaffold49652_822296_SNP 822296 A T scaffold49652_822527_SNP 822527 C A scaffold49652_824023_SNP 824023 T C scaffold49652_824548_SNP 824548 C T scaffold49652_827798_SNP 827798 C G scaffold49652_832297_SNP 832297 T A scaffold49652_833104_SNP 833104 A T scaffold49652_833445_SNP 833445 A G scaffold49652_834051_SNP 834051 G T scaffold49652_840395_SNP 840395 G A scaffold49652_843919_SNP 843919 T C scaffold49652_844263_SNP 844263 T G scaffold49652_849536_SNP 849536 G C scaffold49652_853686_SNP 853686 G A scaffold49652_853931_SNP 853931 G A scaffold49652_854014_SNP 854014 T C scaffold49652_854088_SNP 854088 G T scaffold49652_855619_SNP 855619 T C scaffold49652_860176_SNP 860176 A G scaffold49652_860721_SNP 860721 C T scaffold49652_866753_SNP 866753 T C scaffold49652_868488_SNP 868488 T A scaffold49652_875802_SNP 875802 G C scaffold49652_876164_SNP 876164 A G scaffold49652_879195_SNP 879195 T C scaffold49652_879309_SNP 879309 A G scaffold49652_881100_SNP 881100 G A scaffold49652_881391_SNP 881391 C T scaffold49652_882276_SNP 882276 C T scaffold49652_883184_SNP 883184 G A scaffold49652_883722_SNP 883722 A T scaffold49652_883731_SNP 883731 A T scaffold49652_883732_SNP 883732 T C scaffold49652_883744_SNP 883744 G A scaffold49652_883848_SNP 883848 G A scaffold49652_883854_SNP 883854 T C scaffold49652_883889_SNP 883889 G A scaffold49652_884086_SNP 884086 C A scaffold49652_884823_SNP 884823 C G scaffold49652_885116_SNP 885116 T G scaffold49652_885850_SNP 885850 A G scaffold49652_885852_SNP 885852 G C scaffold49652_885862_SNP 885862 A G scaffold49652_886294_SNP 886294 G C scaffold49652_886462_SNP 886462 C T scaffold49652_886996_SNP 886996 G A scaffold49652_887437_SNP 887437 A T scaffold49652_888216_SNP 888216 G A scaffold49652_888454_SNP 888454 A G scaffold49652_888727_SNP 888727 T A scaffold49652_889850_SNP 889850 T A scaffold49652_891032_SNP 891032 G C scaffold49652_892594_SNP 892594 A G scaffold49652_893679_SNP 893679 G A scaffold49652_893906_SNP 893906 G A scaffold49652_896197_SNP 896197 G A scaffold49652_897517_SNP 897517 A C scaffold49652_897932_SNP 897932 G C scaffold49652_898111_SNP 898111 C A scaffold49652_898112_SNP 898112 G A scaffold49652_898655_SNP 898655 T C scaffold49652_898950_SNP 898950 T C scaffold49652_899021_SNP 899021 G A scaffold49652_899148_SNP 899148 A G scaffold49652_899227_SNP 899227 G T scaffold49652_899335_SNP 899335 A T scaffold49652_899543_SNP 899543 T G scaffold49652_899625_SNP 899625 G T scaffold49652_900624_SNP 900624 C T scaffold49652_901177_SNP 901177 G A scaffold49652_901340_SNP 901340 T C scaffold49652_902549_SNP 902549 C A scaffold49652_903454_SNP 903454 T C scaffold49652_905830_SNP 905830 C T scaffold49652_905860_SNP 905860 G A scaffold49652_906056_SNP 906056 T A scaffold49652_906604_SNP 906604 A G scaffold49652_908695_SNP 908695 C T scaffold49652_909403_SNP 909403 C T scaffold49652_911183_SNP 911183 T C scaffold49652_911607_SNP 911607 A G scaffold49652_911780_SNP 911780 T C scaffold49652_920299_SNP 920299 A G scaffold49652_923770_SNP 923770 C A scaffold49652_924722_SNP 924722 G A scaffold49652_926562_SNP 926562 A T scaffold49652_927214_SNP 927214 G A scaffold49652_943083_SNP 943083 T G scaffold49652_948039_SNP 948039 G A scaffold49652_950135_SNP 950135 C T scaffold49652_951616_SNP 951616 C A scaffold49652_957995_SNP 957995 C T scaffold49652_958508_SNP 958508 A C scaffold49652_967938_SNP 967938 C A scaffold49652_968437_SNP 968437 T C scaffold49652_974414_SNP 974414 C A scaffold49652_979062_SNP 979062 C T scaffold49652_981337_SNP 981337 G A scaffold49652_982834_SNP 982834 G A scaffold49652_998825_SNP 998825 T G scaffold49652_1012367_SNP 1012367 A T scaffold49652_1019615_SNP 1019615 T C scaffold49652_1025554_SNP 1025554 A G scaffold49652_1026033_SNP 1026033 A G scaffold49652_1033935_SNP 1033935 G A scaffold49652_1035086_SNP 1035086 A G scaffold49652_1039213_SNP 1039213 T A scaffold49652_1040045_SNP 1040045 A C scaffold49652_1050328_SNP 1050328 C T scaffold49652_1060132_SNP 1060132 A T scaffold49652_1065677_SNP 1065677 G A scaffold49652_1065813_SNP 1065813 G A scaffold49652_1068136_SNP 1068136 T C scaffold49652_1077026_SNP 1077026 G C scaffold49652_1079091_SNP 1079091 A G scaffold49652_1089823_SNP 1089823 T C scaffold49652_1090444_SNP 1090444 A G scaffold49652_1091054_SNP 1091054 T C scaffold49652_1094373_SNP 1094373 G T scaffold49652_1094567_SNP 1094567 T A scaffold49652_1095586_SNP 1095586 G T scaffold49652_1096330_SNP 1096330 C G scaffold49652_1096345_SNP 1096345 C T scaffold49652_1097283_SNP 1097283 T A scaffold49652_1098183_SNP 1098183 T C scaffold49652_1098188_SNP 1098188 T C scaffold49652_1098428_SNP 1098428 G A scaffold49652_1098776_SNP 1098776 G A scaffold49652_1098789_SNP 1098789 G A scaffold49652_1099064_SNP 1099064 G C scaffold49652_1099104_SNP 1099104 A G scaffold49652_1099204_SNP 1099204 C G scaffold49652_1099381_SNP 1099381 C A scaffold49652_1101177_SNP 1101177 G A scaffold49652_1105870_SNP 1105870 G A scaffold49652_1106259_SNP 1106259 T C scaffold49652_1106268_SNP 1106268 T G scaffold49652_1107450_SNP 1107450 A T scaffold49652_1111008_SNP 1111008 C A scaffold49652_1113214_SNP 1113214 T G scaffold49652_1115505_SNP 1115505 C T scaffold49652_1115579_SNP 1115579 G A scaffold49652_1117895_SNP 1117895 C A scaffold49652_1118621_SNP 1118621 A G scaffold49652_1119640_SNP 1119640 A G scaffold49652_1120313_SNP 1120313 T C scaffold49652_1120591_SNP 1120591 G A scaffold49652_1120734_SNP 1120734 T C scaffold49652_1120836_SNP 1120836 G A scaffold49652_1121086_SNP 1121086 A G scaffold49652_1121309_SNP 1121309 T C scaffold49652_1122559_SNP 1122559 A T scaffold49652_1123165_SNP 1123165 A C scaffold49652_1124824_SNP 1124824 A G scaffold49652_1125027_SNP 1125027 C G scaffold49652_1125210_SNP 1125210 T C scaffold49652_1125225_SNP 1125225 T C scaffold49652_1125331_SNP 1125331 A G scaffold49652_1125495_SNP 1125495 C T scaffold49652_1125680_SNP 1125680 C G scaffold49652_1126353_SNP 1126353 T A scaffold49652_1126379_SNP 1126379 A T scaffold49652_1126987_SNP 1126987 G T scaffold49652_1128639_SNP 1128639 T G scaffold49652_1130083_SNP 1130083 A T scaffold49652_1132532_SNP 1132532 T C scaffold49652_1133562_SNP 1133562 C A scaffold49652_1138025_SNP 1138025 A G scaffold49652_1138114_SNP 1138114 A G scaffold49652_1138128_SNP 1138128 T C scaffold49652_1138158_SNP 1138158 C A scaffold49652_1138340_SNP 1138340 A C scaffold49652_1138444_SNP 1138444 A T scaffold49652_1138486_SNP 1138486 G T scaffold49652_1138569_SNP 1138569 C T scaffold49652_1138892_SNP 1138892 G A scaffold49652_1138915_SNP 1138915 T C scaffold49652_1138942_SNP 1138942 T G scaffold49652_1138948_SNP 1138948 A G scaffold49652_1138972_SNP 1138972 T C scaffold49652_1143904_SNP 1143904 T A scaffold49652_1145401_SNP 1145401 G A scaffold49652_1145644_SNP 1145644 A G scaffold49652_1147593_SNP 1147593 T C scaffold49652_1149884_SNP 1149884 T G scaffold49652_1156135_SNP 1156135 C T scaffold49652_1156749_SNP 1156749 T A scaffold49652_1160712_SNP 1160712 T C scaffold49652_1161165_SNP 1161165 A G scaffold49652_1161234_SNP 1161234 A C scaffold49652_1161762_SNP 1161762 C A scaffold49652_1161951_SNP 1161951 C T scaffold49652_1161984_SNP 1161984 C T scaffold49652_1161994_SNP 1161994 C T scaffold49652_1162010_SNP 1162010 T C scaffold49652_1162087_SNP 1162087 T A scaffold49652_1162117_SNP 1162117 C T scaffold49652_1163148_SNP 1163148 G A scaffold49652_1163858_SNP 1163858 C T scaffold49652_1165241_SNP 1165241 A G scaffold49652_1165983_SNP 1165983 G A scaffold49652_1166553_SNP 1166553 T G scaffold49652_1167905_SNP 1167905 G A scaffold49652_1168063_SNP 1168063 G C scaffold49652_1168123_SNP 1168123 C G scaffold49652_1168144_SNP 1168144 G A scaffold49652_1168354_SNP 1168354 G A scaffold49652_1168382_SNP 1168382 A G scaffold49652_1168402_SNP 1168402 C T scaffold49652_1168415_SNP 1168415 C G scaffold49652_1168591_SNP 1168591 A G scaffold49652_1168598_SNP 1168598 T C scaffold49652_1168676_SNP 1168676 A G scaffold49652_1173678_SNP 1173678 C T scaffold49652_1174439_SNP 1174439 G A scaffold49652_1174739_SNP 1174739 T C scaffold49652_1174886_SNP 1174886 G C scaffold49652_1174957_SNP 1174957 T C scaffold49652_1175137_SNP 1175137 T C scaffold49652_1176562_SNP 1176562 T C scaffold49652_1176601_SNP 1176601 A G scaffold49652_1176744_SNP 1176744 A G scaffold49652_1176824_SNP 1176824 T C scaffold49652_1176918_SNP 1176918 T A scaffold49652_1177011_SNP 1177011 T C scaffold49652_1177564_SNP 1177564 C T scaffold49652_1178504_SNP 1178504 G C scaffold49652_1178688_SNP 1178688 G A scaffold49652_1178845_SNP 1178845 T C scaffold49652_1180897_SNP 1180897 G C scaffold49652_1181191_SNP 1181191 C A scaffold49652_1182912_SNP 1182912 A T scaffold49652_1185115_SNP 1185115 A T scaffold49652_1185149_SNP 1185149 G A scaffold49652_1185173_SNP 1185173 T C scaffold49652_1185483_SNP 1185483 A G scaffold49652_1185495_SNP 1185495 A G scaffold49652_1185519_SNP 1185519 C T scaffold49652_1185550_SNP 1185550 C T scaffold49652_1186445_SNP 1186445 T A scaffold49652_1187282_SNP 1187282 T C scaffold49652_1187782_SNP 1187782 C T scaffold49652_1187807_SNP 1187807 G C scaffold49652_1187833_SNP 1187833 A G scaffold49652_1187867_SNP 1187867 C T scaffold49652_1189518_SNP 1189518 A G scaffold49652_1195840_SNP 1195840 C A scaffold49652_1197189_SNP 1197189 G A scaffold49652_1197456_SNP 1197456 A G scaffold49652_1197501_SNP 1197501 T G scaffold49652_1198166_SNP 1198166 A G scaffold49652_1198222_SNP 1198222 A C scaffold49652_1198541_SNP 1198541 A T scaffold49652_1198622_SNP 1198622 A T scaffold49652_1198980_SNP 1198980 C T scaffold49652_1199022_SNP 1199022 T C scaffold49652_1199906_SNP 1199906 A C scaffold49652_1200447_SNP 1200447 A G scaffold49652_1201288_SNP 1201288 T C scaffold49652_1201696_SNP 1201696 C T scaffold49652_1201765_SNP 1201765 T G scaffold49652_1202166_SNP 1202166 C T scaffold49652_1202941_SNP 1202941 T G scaffold49652_1203263_SNP 1203263 C T scaffold49652_1203989_SNP 1203989 G A scaffold49652_1204064_SNP 1204064 G A scaffold49652_1204476_SNP 1204476 T C scaffold49652_1204977_SNP 1204977 A T scaffold49652_1205446_SNP 1205446 A G scaffold49652_1205510_SNP 1205510 A G scaffold49652_1205721_SNP 1205721 A G scaffold49652_1205762_SNP 1205762 T A scaffold49652_1205797_SNP 1205797 A C scaffold49652_1205865_SNP 1205865 T A scaffold49652_1205903_SNP 1205903 A G scaffold49652_1206037_SNP 1206037 T G scaffold49652_1206135_SNP 1206135 A T scaffold49652_1206148_SNP 1206148 T C scaffold49652_1206150_SNP 1206150 A T scaffold49652_1206333_SNP 1206333 A G scaffold49652_1206709_SNP 1206709 A G scaffold49652_1207012_SNP 1207012 G A scaffold49652_1207348_SNP 1207348 A G scaffold49652_1207374_SNP 1207374 C A scaffold49652_1207430_SNP 1207430 T A scaffold49652_1207492_SNP 1207492 G A scaffold49652_1207513_SNP 1207513 C T scaffold49652_1209506_SNP 1209506 G C scaffold49652_1209518_SNP 1209518 T C scaffold49652_1209544_SNP 1209544 A G scaffold49652_1211198_SNP 1211198 T C scaffold49652_1211200_SNP 1211200 T A scaffold49652_1213512_SNP 1213512 T C scaffold49652_1214402_SNP 1214402 G A scaffold49652_1215784_SNP 1215784 T A scaffold49652_1216069_SNP 1216069 G A scaffold49652_1217956_SNP 1217956 T C scaffold49652_1219424_SNP 1219424 G A scaffold49652_1220232_SNP 1220232 A G scaffold49652_1220233_SNP 1220233 C T scaffold49652_1221995_SNP 1221995 C T scaffold49652_1222469_SNP 1222469 T C scaffold49652_1222668_SNP 1222668 T C scaffold49652_1224176_SNP 1224176 A G scaffold49652_1225431_SNP 1225431 A C scaffold49652_1227822_SNP 1227822 G T scaffold49652_1229006_SNP 1229006 G A scaffold49652_1229064_SNP 1229064 T C scaffold49652_1229326_SNP 1229326 C G scaffold49652_1231604_SNP 1231604 T C scaffold49652_1232591_SNP 1232591 G C scaffold49652_1233258_SNP 1233258 T C scaffold49652_1233269_SNP 1233269 G A scaffold49652_1233617_SNP 1233617 G A scaffold49652_1233633_SNP 1233633 T C scaffold49652_1234922_SNP 1234922 A C scaffold49652_1235646_SNP 1235646 T C scaffold49652_1242212_SNP 1242212 T G scaffold49652_1245007_SNP 1245007 C T scaffold49652_1245040_SNP 1245040 A G scaffold49652_1247417_SNP 1247417 A T scaffold49652_1248388_SNP 1248388 A C scaffold49652_1249563_SNP 1249563 C T scaffold49652_1249616_SNP 1249616 G A scaffold49652_1249760_SNP 1249760 G A scaffold49652_1249992_SNP 1249992 G A scaffold49652_1253370_SNP 1253370 T G scaffold49652_1254006_SNP 1254006 C T scaffold49652_1257900_SNP 1257900 A G scaffold49652_1260621_SNP 1260621 G C scaffold49652_1260771_SNP 1260771 T C scaffold49652_1261627_SNP 1261627 A T scaffold49652_1261954_SNP 1261954 C A scaffold49652_1262618_SNP 1262618 A C scaffold49652_1262670_SNP 1262670 G C scaffold49652_1263002_SNP 1263002 T C scaffold49652_1263917_SNP 1263917 T C scaffold49652_1263984_SNP 1263984 G T scaffold49652_1265551_SNP 1265551 G C scaffold49652_1266148_SNP 1266148 A G scaffold49652_1266149_SNP 1266149 G A scaffold49652_1266165_SNP 1266165 T C scaffold49652_1266173_SNP 1266173 G A scaffold49652_1266252_SNP 1266252 T C scaffold49652_1267716_SNP 1267716 T C scaffold49652_1268719_SNP 1268719 T A scaffold49652_1269754_SNP 1269754 A G scaffold49652_1272386_SNP 1272386 C G scaffold49652_1274965_SNP 1274965 C T scaffold49652_1275187_SNP 1275187 G C scaffold49652_1275978_SNP 1275978 G A scaffold49652_1276158_SNP 1276158 A G scaffold49652_1285645_SNP 1285645 C T scaffold49652_1285703_SNP 1285703 G A scaffold49652_1287076_SNP 1287076 T A scaffold49652_1287285_SNP 1287285 A G scaffold49652_1287342_SNP 1287342 C T scaffold49652_1288020_SNP 1288020 A G scaffold49652_1288039_SNP 1288039 C A scaffold49652_1288110_SNP 1288110 G A scaffold49652_1288261_SNP 1288261 G T scaffold49652_1288298_SNP 1288298 A G scaffold49652_1288817_SNP 1288817 T C scaffold49652_1289315_SNP 1289315 A G scaffold49652_1289365_SNP 1289365 A G scaffold49652_1290541_SNP 1290541 C A scaffold49652_1290877_SNP 1290877 C T scaffold49652_1292092_SNP 1292092 G T scaffold49652_1296215_SNP 1296215 T G scaffold49652_1300497_SNP 1300497 A C scaffold49652_1301168_SNP 1301168 T G scaffold49652_1301459_SNP 1301459 G T scaffold49652_1304023_SNP 1304023 T C scaffold49652_1304442_SNP 1304442 T A scaffold49652_1305544_SNP 1305544 G A scaffold49652_1305909_SNP 1305909 T C scaffold49652_1307320_SNP 1307320 A G scaffold49652_1308573_SNP 1308573 T G scaffold49652_1309111_SNP 1309111 A T scaffold49652_1309910_SNP 1309910 A G scaffold49652_1310627_SNP 1310627 A G scaffold49652_1311366_SNP 1311366 A G scaffold49652_1311661_SNP 1311661 G C scaffold49652_1312620_SNP 1312620 G A scaffold49652_1312688_SNP 1312688 A T scaffold49652_1314839_SNP 1314839 G A scaffold49652_1318161_SNP 1318161 G A scaffold49652_1319905_SNP 1319905 T A scaffold49652_1319927_SNP 1319927 A T scaffold49652_1325373_SNP 1325373 A G scaffold49652_1327039_SNP 1327039 C A scaffold49652_1327125_SNP 1327125 G A scaffold49652_1330359_SNP 1330359 C T scaffold49652_1330510_SNP 1330510 G A scaffold49652_1330691_SNP 1330691 C T scaffold49652_1331569_SNP 1331569 G A scaffold49652_1337671_SNP 1337671 A C scaffold49652_1338851_SNP 1338851 T C scaffold49652_1342039_SNP 1342039 T C scaffold49652_1349150_SNP 1349150 T G scaffold49652_1349305_SNP 1349305 C G scaffold49652_1349459_SNP 1349459 G A scaffold49652_1350228_SNP 1350228 C A scaffold49652_1350475_SNP 1350475 A T scaffold49652_1350767_SNP 1350767 A G scaffold49652_1350817_SNP 1350817 G A scaffold49652_1351683_SNP 1351683 C T scaffold49652_1351871_SNP 1351871 T C scaffold49652_1353291_SNP 1353291 C T scaffold49652_1355147_SNP 1355147 A C scaffold49652_1355187_SNP 1355187 A G scaffold49652_1355230_SNP 1355230 T C scaffold49652_1355250_SNP 1355250 A G scaffold49652_1355677_SNP 1355677 T A scaffold49652_1356300_SNP 1356300 T C scaffold49652_1356305_SNP 1356305 G A scaffold49652_1356320_SNP 1356320 G C scaffold49652_1359144_SNP 1359144 T A scaffold49652_1359155_SNP 1359155 A T scaffold49652_1360507_SNP 1360507 A G scaffold49652_1360522_SNP 1360522 C T scaffold49652_1360564_SNP 1360564 A G scaffold49652_1360872_SNP 1360872 C T scaffold49652_1370489_SNP 1370489 A G scaffold49652_1370564_SNP 1370564 A G scaffold49652_1372158_SNP 1372158 G C scaffold49652_1372159_SNP 1372159 T C scaffold49652_1373213_SNP 1373213 C A scaffold49652_1377409_SNP 1377409 T C scaffold49652_1378219_SNP 1378219 A C scaffold49652_1379478_SNP 1379478 A G scaffold49652_1379538_SNP 1379538 T A scaffold49652_1380960_SNP 1380960 T C scaffold49652_1381295_SNP 1381295 G A scaffold49652_1381522_SNP 1381522 G A scaffold49652_1381720_SNP 1381720 G A scaffold49652_1382796_SNP 1382796 A G scaffold49652_1384076_SNP 1384076 C T scaffold49652_1384083_SNP 1384083 C T scaffold49652_1384210_SNP 1384210 G A scaffold49652_1384225_SNP 1384225 T C scaffold49652_1384233_SNP 1384233 A G scaffold49652_1384646_SNP 1384646 C G scaffold49652_1386487_SNP 1386487 C T scaffold49652_1387398_SNP 1387398 T C scaffold49652_1388592_SNP 1388592 T C scaffold49652_1389373_SNP 1389373 A G scaffold49652_1390362_SNP 1390362 C T scaffold49652_1390399_SNP 1390399 C A scaffold49652_1391282_SNP 1391282 G T scaffold49652_1391283_SNP 1391283 G T scaffold49652_1391328_SNP 1391328 A G scaffold49652_1391432_SNP 1391432 G A scaffold49652_1392482_SNP 1392482 T G scaffold49652_1393382_SNP 1393382 A G scaffold49652_1394841_SNP 1394841 A G scaffold49652_1395450_SNP 1395450 C A scaffold49652_1396427_SNP 1396427 G T scaffold49652_1397384_SNP 1397384 G C scaffold49652_1397840_SNP 1397840 C T scaffold49652_1398988_SNP 1398988 G T scaffold49652_1398997_SNP 1398997 A C scaffold49652_1400236_SNP 1400236 T C scaffold49652_1406135_SNP 1406135 C T scaffold49652_1406929_SNP 1406929 T C scaffold49652_1406970_SNP 1406970 G A scaffold49652_1412574_SNP 1412574 G A scaffold49652_1412984_SNP 1412984 A G scaffold49652_1413190_SNP 1413190 T G scaffold49652_1413578_SNP 1413578 T A scaffold49652_1414567_SNP 1414567 T A scaffold49652_1414947_SNP 1414947 T A scaffold49652_1415171_SNP 1415171 A G scaffold49652_1420459_SNP 1420459 G A scaffold49652_1425012_SNP 1425012 A G scaffold49652_1425787_SNP 1425787 A T scaffold49652_1427691_SNP 1427691 A T scaffold49652_1439691_SNP 1439691 G T scaffold49652_1441763_SNP 1441763 A T scaffold49652_1446012_SNP 1446012 T A scaffold49652_1448318_SNP 1448318 G A scaffold49652_1452330_SNP 1452330 T C scaffold49652_1455958_SNP 1455958 A G scaffold49652_1458870_SNP 1458870 T A scaffold49652_1459287_SNP 1459287 C A scaffold49652_1464696_SNP 1464696 C T scaffold49652_1473688_SNP 1473688 C A scaffold49652_1477682_SNP 1477682 A C scaffold49652_1482016_SNP 1482016 G A scaffold49652_1484394_SNP 1484394 G A scaffold49652_1484736_SNP 1484736 A T scaffold49652_1486437_SNP 1486437 T A scaffold49652_1486718_SNP 1486718 A G scaffold49652_1487392_SNP 1487392 A C scaffold49652_1490346_SNP 1490346 A G scaffold49652_1490664_SNP 1490664 A T scaffold49652_1497465_SNP 1497465 G A scaffold49652_1498098_SNP 1498098 A G scaffold49652_1498277_SNP 1498277 G A scaffold49652_1498726_SNP 1498726 A C scaffold49652_1498730_SNP 1498730 G A scaffold49652_1498784_SNP 1498784 C T scaffold49652_1499589_SNP 1499589 T C scaffold49652_1499694_SNP 1499694 C A scaffold49652_1499831_SNP 1499831 T C scaffold49652_1499964_SNP 1499964 G C scaffold49652_1500119_SNP 1500119 C T scaffold49652_1500300_SNP 1500300 G A scaffold49652_1500589_SNP 1500589 C T scaffold49652_1500834_SNP 1500834 G A scaffold49652_1501563_SNP 1501563 G C scaffold49652_1501587_SNP 1501587 A C scaffold49652_1501646_SNP 1501646 C T scaffold49652_1502068_SNP 1502068 T G scaffold49652_1502597_SNP 1502597 A G scaffold49652_1502635_SNP 1502635 C A scaffold49652_1503077_SNP 1503077 C A scaffold49652_1503219_SNP 1503219 G A scaffold49652_1503270_SNP 1503270 T C scaffold49652_1503416_SNP 1503416 G T scaffold49652_1503427_SNP 1503427 T C scaffold49652_1503442_SNP 1503442 C A scaffold49652_1503443_SNP 1503443 G A scaffold49652_1503849_SNP 1503849 A C scaffold49652_1504038_SNP 1504038 A G scaffold49652_1504047_SNP 1504047 C G scaffold49652_1504065_SNP 1504065 G A scaffold49652_1504101_SNP 1504101 C T scaffold49652_1504276_SNP 1504276 G C scaffold49652_1504328_SNP 1504328 A C scaffold49652_1504542_SNP 1504542 C T scaffold49652_1504575_SNP 1504575 A T scaffold49652_1504595_SNP 1504595 T C scaffold49652_1504723_SNP 1504723 T G scaffold49652_1505015_SNP 1505015 A T scaffold49652_1505026_SNP 1505026 G A scaffold49652_1505111_SNP 1505111 T A scaffold49652_1505201_SNP 1505201 G A scaffold49652_1505243_SNP 1505243 G A scaffold49652_1506602_SNP 1506602 G C scaffold49652_1506823_SNP 1506823 C T scaffold49652_1506945_SNP 1506945 C T scaffold49652_1507115_SNP 1507115 A C scaffold49652_1507459_SNP 1507459 A G scaffold49652_1508337_SNP 1508337 A C scaffold49652_1508384_SNP 1508384 C A scaffold49652_1508840_SNP 1508840 G A scaffold49652_1509261_SNP 1509261 C T scaffold49652_1509579_SNP 1509579 T A scaffold49652_1509633_SNP 1509633 A G scaffold49652_1509837_SNP 1509837 A C scaffold49652_1509840_SNP 1509840 T C scaffold49652_1510029_SNP 1510029 G T scaffold49652_1510081_SNP 1510081 G A scaffold49652_1510310_SNP 1510310 G A scaffold49652_1510352_SNP 1510352 A G scaffold49652_1510865_SNP 1510865 C T scaffold49652_1511280_SNP 1511280 T C scaffold49652_1511395_SNP 1511395 T C scaffold49652_1511421_SNP 1511421 C A scaffold49652_1511424_SNP 1511424 A T scaffold49652_1511426_SNP 1511426 C T scaffold49652_1511469_SNP 1511469 C T scaffold49652_1511592_SNP 1511592 T A scaffold49652_1511657_SNP 1511657 T G scaffold49652_1511748_SNP 1511748 G C scaffold49652_1511995_SNP 1511995 C A scaffold49652_1512321_SNP 1512321 T G scaffold49652_1512638_SNP 1512638 A G scaffold49652_1512709_SNP 1512709 C T scaffold49652_1519579_SNP 1519579 T C scaffold49652_1525812_SNP 1525812 G T scaffold49652_1526777_SNP 1526777 T C scaffold49652_1527451_SNP 1527451 A C scaffold49652_1527474_SNP 1527474 T C scaffold49652_1527528_SNP 1527528 A G scaffold49652_1527697_SNP 1527697 G C scaffold49652_1529671_SNP 1529671 G A scaffold49652_1529889_SNP 1529889 C A scaffold49652_1529893_SNP 1529893 G T scaffold49652_1530108_SNP 1530108 A C scaffold49652_1532466_SNP 1532466 T C scaffold49652_1533033_SNP 1533033 C T scaffold49652_1533101_SNP 1533101 T A scaffold49652_1533473_SNP 1533473 G C scaffold49652_1533647_SNP 1533647 A C scaffold49652_1533653_SNP 1533653 T C scaffold49652_1533761_SNP 1533761 G A scaffold49652_1533817_SNP 1533817 T C scaffold49652_1533820_SNP 1533820 G T scaffold49652_1533913_SNP 1533913 C T scaffold49652_1533992_SNP 1533992 A T scaffold49652_1534122_SNP 1534122 C T scaffold49652_1534370_SNP 1534370 G A scaffold49652_1534594_SNP 1534594 G T scaffold49652_1534861_SNP 1534861 C T scaffold49652_1534901_SNP 1534901 T C scaffold49652_1534951_SNP 1534951 T G scaffold49652_1534973_SNP 1534973 T C scaffold49652_1535397_SNP 1535397 T A scaffold49652_1535471_SNP 1535471 A G scaffold49652_1535713_SNP 1535713 G C scaffold49652_1535759_SNP 1535759 G T scaffold49652_1535787_SNP 1535787 T C scaffold49652_1536164_SNP 1536164 T A scaffold49652_1536203_SNP 1536203 C T scaffold49652_1536208_SNP 1536208 C T scaffold49652_1536258_SNP 1536258 A G scaffold49652_1536492_SNP 1536492 T A scaffold49652_1536668_SNP 1536668 G T scaffold49652_1536874_SNP 1536874 C G scaffold49652_1536947_SNP 1536947 G A scaffold49652_1537026_SNP 1537026 T C scaffold49652_1537049_SNP 1537049 G T scaffold49652_1537209_SNP 1537209 C T scaffold49652_1537396_SNP 1537396 C T scaffold49652_1537400_SNP 1537400 A G scaffold49652_1537466_SNP 1537466 G A scaffold49652_1537469_SNP 1537469 A G scaffold49652_1537508_SNP 1537508 T C scaffold49652_1537761_SNP 1537761 A C scaffold49652_1537782_SNP 1537782 G T scaffold49652_1538460_SNP 1538460 T A scaffold49652_1538522_SNP 1538522 G A scaffold49652_1539298_SNP 1539298 T C scaffold49652_1539596_SNP 1539596 G A scaffold49652_1539844_SNP 1539844 A G scaffold49652_1539846_SNP 1539846 T C scaffold49652_1540106_SNP 1540106 C T scaffold49652_1540355_SNP 1540355 T A scaffold49652_1540361_SNP 1540361 T C scaffold49652_1542105_SNP 1542105 G T scaffold49652_1542192_SNP 1542192 A G scaffold49652_1542903_SNP 1542903 T C scaffold49652_1542948_SNP 1542948 G A scaffold49652_1542985_SNP 1542985 A G scaffold49652_1543326_SNP 1543326 G A scaffold49652_1543480_SNP 1543480 T C scaffold49652_1543521_SNP 1543521 T C scaffold49652_1543573_SNP 1543573 G A scaffold49652_1544029_SNP 1544029 G T scaffold49652_1544098_SNP 1544098 G A scaffold49652_1544113_SNP 1544113 C T scaffold49652_1544156_SNP 1544156 C T scaffold49652_1544767_SNP 1544767 A G scaffold49652_1544768_SNP 1544768 C A scaffold49652_1545344_SNP 1545344 T C scaffold49652_1545580_SNP 1545580 C T scaffold49652_1545677_SNP 1545677 G C scaffold49652_1546183_SNP 1546183 T G scaffold49652_1546253_SNP 1546253 G C scaffold49652_1547303_SNP 1547303 G T scaffold49652_1549454_SNP 1549454 G C scaffold49652_1550953_SNP 1550953 G T scaffold49652_1551454_SNP 1551454 G T scaffold49652_1551466_SNP 1551466 C G scaffold49652_1551516_SNP 1551516 C T scaffold49652_1551524_SNP 1551524 T C scaffold49652_1551889_SNP 1551889 T C scaffold49652_1551893_SNP 1551893 A T scaffold49652_1552041_SNP 1552041 A C scaffold49652_1552920_SNP 1552920 G C scaffold49652_1553019_SNP 1553019 A T scaffold49652_1553020_SNP 1553020 C T scaffold49652_1553247_SNP 1553247 G A scaffold49652_1553264_SNP 1553264 A C scaffold49652_1553305_SNP 1553305 T C scaffold49652_1553323_SNP 1553323 C G scaffold49652_1553641_SNP 1553641 C G scaffold49652_1554381_SNP 1554381 A G scaffold49652_1554522_SNP 1554522 A C scaffold49652_1555756_SNP 1555756 C A scaffold49652_1555802_SNP 1555802 A G scaffold49652_1556023_SNP 1556023 A T scaffold49652_1556301_SNP 1556301 T C scaffold49652_1556314_SNP 1556314 G A scaffold49652_1556354_SNP 1556354 G A scaffold49652_1556356_SNP 1556356 C T scaffold49652_1556398_SNP 1556398 C T scaffold49652_1556825_SNP 1556825 C G scaffold49652_1557388_SNP 1557388 T C scaffold49652_1557402_SNP 1557402 A C scaffold49652_1557403_SNP 1557403 G T scaffold49652_1558327_SNP 1558327 G A scaffold49652_1558999_SNP 1558999 C T scaffold49652_1559045_SNP 1559045 T G scaffold49652_1559075_SNP 1559075 T A scaffold49652_1559076_SNP 1559076 T A scaffold49652_1559133_SNP 1559133 T C scaffold49652_1561075_SNP 1561075 A G scaffold49652_1563948_SNP 1563948 C T scaffold49652_1563987_SNP 1563987 G A scaffold49652_1564295_SNP 1564295 G A scaffold49652_1564405_SNP 1564405 G T scaffold49652_1564547_SNP 1564547 A G scaffold49652_1564651_SNP 1564651 C G scaffold49652_1564876_SNP 1564876 A C scaffold49652_1565656_SNP 1565656 G A scaffold49652_1566960_SNP 1566960 G A scaffold49652_1568459_SNP 1568459 G A scaffold49652_1568469_SNP 1568469 T C scaffold49652_1568476_SNP 1568476 G A scaffold49652_1568909_SNP 1568909 T C scaffold49652_1569191_SNP 1569191 A G scaffold49652_1569222_SNP 1569222 C T scaffold49652_1569352_SNP 1569352 G A scaffold49652_1569521_SNP 1569521 C T scaffold49652_1569522_SNP 1569522 C T scaffold49652_1569581_SNP 1569581 C T scaffold49652_1569654_SNP 1569654 T G scaffold49652_1569941_SNP 1569941 G T scaffold49652_1569964_SNP 1569964 G A scaffold49652_1570030_SNP 1570030 A G scaffold49652_1570384_SNP 1570384 T A scaffold49652_1570684_SNP 1570684 T G scaffold49652_1570738_SNP 1570738 G A scaffold49652_1571106_SNP 1571106 C A scaffold49652_1571967_SNP 1571967 T C scaffold49652_1572221_SNP 1572221 C A scaffold49652_1572383_SNP 1572383 T A scaffold49652_1572517_SNP 1572517 G A scaffold49652_1573983_SNP 1573983 C A scaffold49652_1574213_SNP 1574213 T C scaffold49652_1574333_SNP 1574333 G A scaffold49652_1574676_SNP 1574676 G A scaffold49652_1574783_SNP 1574783 G T scaffold49652_1574817_SNP 1574817 T C scaffold49652_1574821_SNP 1574821 A T scaffold49652_1576691_SNP 1576691 G A scaffold49652_1578153_SNP 1578153 T C scaffold49652_1578410_SNP 1578410 T A scaffold49652_1579480_SNP 1579480 G A scaffold49652_1580162_SNP 1580162 G A scaffold49652_1585124_SNP 1585124 G A scaffold49652_1591552_SNP 1591552 G C scaffold49652_1593734_SNP 1593734 T A scaffold49652_1593979_SNP 1593979 G A scaffold49652_1594860_SNP 1594860 A G scaffold49652_1595032_SNP 1595032 C T scaffold49652_1596156_SNP 1596156 T C scaffold49652_1598089_SNP 1598089 C A scaffold49652_1598664_SNP 1598664 T C scaffold49652_1600217_SNP 1600217 G C scaffold49652_1600861_SNP 1600861 T G scaffold49652_1601108_SNP 1601108 A G scaffold49652_1606896_SNP 1606896 G A scaffold49652_1606901_SNP 1606901 A C scaffold49652_1606946_SNP 1606946 A T scaffold49652_1607051_SNP 1607051 C T scaffold49652_1607970_SNP 1607970 A T scaffold49652_1608931_SNP 1608931 C T scaffold49652_1611052_SNP 1611052 C G scaffold49652_1611319_SNP 1611319 T C scaffold49652_1611324_SNP 1611324 G T scaffold49652_1611669_SNP 1611669 T C scaffold49652_1612160_SNP 1612160 G A scaffold49652_1612262_SNP 1612262 A G scaffold49652_1612278_SNP 1612278 T G scaffold49652_1612872_SNP 1612872 A G scaffold49652_1613879_SNP 1613879 C T scaffold49652_1614448_SNP 1614448 G A scaffold49652_1614630_SNP 1614630 A G scaffold49652_1615422_SNP 1615422 T C scaffold49652_1615483_SNP 1615483 C A scaffold49652_1615540_SNP 1615540 T C scaffold49652_1615851_SNP 1615851 T C scaffold49652_1615852_SNP 1615852 G A scaffold49652_1616125_SNP 1616125 G A scaffold49652_1616178_SNP 1616178 A G scaffold49652_1616195_SNP 1616195 A G scaffold49652_1616403_SNP 1616403 G A scaffold49652_1617007_SNP 1617007 T G scaffold49652_1617865_SNP 1617865 G C scaffold49652_1618890_SNP 1618890 A C scaffold49652_1618892_SNP 1618892 T A scaffold49652_1619290_SNP 1619290 A G scaffold49652_1619574_SNP 1619574 C A scaffold49652_1619632_SNP 1619632 T G scaffold49652_1619917_SNP 1619917 G A scaffold49652_1621408_SNP 1621408 A G scaffold49652_1621878_SNP 1621878 G A scaffold49652_1622798_SNP 1622798 A G scaffold49652_1622821_SNP 1622821 C T scaffold49652_1626988_SNP 1626988 G A scaffold49652_1627444_SNP 1627444 G A scaffold49652_1627969_SNP 1627969 G A scaffold49652_1628615_SNP 1628615 C T scaffold49652_1630497_SNP 1630497 C G scaffold49652_1631111_SNP 1631111 C G scaffold49652_1631190_SNP 1631190 G C scaffold49652_1631597_SNP 1631597 C G scaffold49652_1632497_SNP 1632497 A G scaffold49652_1633787_SNP 1633787 A G scaffold49652_1635028_SNP 1635028 A C scaffold49652_1635345_SNP 1635345 A T scaffold49652_1636124_SNP 1636124 A G scaffold49652_1637672_SNP 1637672 A G scaffold49652_1637924_SNP 1637924 C T scaffold49652_1638248_SNP 1638248 C A scaffold49652_1638634_SNP 1638634 A G scaffold49652_1639333_SNP 1639333 C G scaffold49652_1639344_SNP 1639344 A T scaffold49652_1640567_SNP 1640567 T A scaffold49652_1640589_SNP 1640589 C T scaffold49652_1641369_SNP 1641369 T A scaffold49652_1642436_SNP 1642436 T C scaffold49652_1642517_SNP 1642517 A G scaffold49652_1642930_SNP 1642930 G T scaffold49652_1645749_SNP 1645749 G A scaffold49652_1645778_SNP 1645778 G A scaffold49652_1646272_SNP 1646272 T C scaffold49652_1648632_SNP 1648632 C T scaffold49652_1650650_SNP 1650650 C T scaffold49652_1653321_SNP 1653321 C T scaffold49652_1653395_SNP 1653395 T G scaffold49652_1653923_SNP 1653923 T A scaffold49652_1654022_SNP 1654022 T C scaffold49652_1654024_SNP 1654024 C T scaffold49652_1654082_SNP 1654082 C A scaffold49652_1654121_SNP 1654121 A G scaffold49652_1657071_SNP 1657071 C T scaffold49652_1657306_SNP 1657306 A G scaffold49652_1657419_SNP 1657419 C G scaffold49652_1659632_SNP 1659632 T C scaffold49652_1659667_SNP 1659667 C T scaffold49652_1660987_SNP 1660987 G T scaffold49652_1662158_SNP 1662158 G C scaffold49652_1668419_SNP 1668419 C T scaffold49652_1673502_SNP 1673502 G T scaffold49652_1683393_SNP 1683393 T C scaffold49652_1691712_SNP 1691712 G A scaffold49652_1706511_SNP 1706511 G C scaffold49652_1706512_SNP 1706512 G A scaffold49652_1708631_SNP 1708631 C T scaffold49652_1714596_SNP 1714596 G A scaffold49652_1715039_SNP 1715039 T C scaffold49652_1717036_SNP 1717036 G A scaffold49652_1724262_SNP 1724262 A C scaffold49652_1726873_SNP 1726873 T A scaffold49652_1728573_SNP 1728573 T C scaffold49652_1729370_SNP 1729370 G A scaffold49652_1731936_SNP 1731936 A G scaffold49652_1731965_SNP 1731965 A G scaffold49652_1733030_SNP 1733030 C T scaffold49652_1733331_SNP 1733331 G A scaffold49652_1733615_SNP 1733615 C T scaffold49652_1744444_SNP 1744444 G A scaffold49652_1744567_SNP 1744567 G T scaffold49652_1749854_SNP 1749854 G A scaffold49652_1752330_SNP 1752330 T A scaffold49652_1760004_SNP 1760004 C T scaffold49652_1764534_SNP 1764534 A G scaffold49652_1781766_SNP 1781766 G C scaffold49652_1781798_SNP 1781798 C G scaffold49652_1782420_SNP 1782420 A C scaffold49652_1784250_SNP 1784250 A G scaffold49652_1790651_SNP 1790651 T G scaffold49652_1801261_SNP 1801261 C T scaffold49652_1803941_SNP 1803941 G A scaffold49652_1817041_SNP 1817041 T A scaffold49652_1823072_SNP 1823072 T C scaffold49652_1830747_SNP 1830747 T C scaffold49652_1833496_SNP 1833496 A G scaffold49652_1834606_SNP 1834606 G A scaffold49652_1837409_SNP 1837409 A G scaffold49652_1843144_SNP 1843144 A G scaffold49652_1846505_SNP 1846505 G A scaffold49652_1846953_SNP 1846953 T C scaffold49652_1846990_SNP 1846990 A C scaffold49652_1847290_SNP 1847290 A G scaffold49652_1848210_SNP 1848210 T C scaffold49652_1848375_SNP 1848375 G T scaffold49652_1848606_SNP 1848606 C A scaffold49652_1850004_SNP 1850004 T C scaffold49652_1850077_SNP 1850077 A G scaffold49652_1851455_SNP 1851455 T C scaffold49652_1853986_SNP 1853986 T C scaffold49652_1854890_SNP 1854890 T G scaffold49652_1858706_SNP 1858706 G T scaffold49652_1859460_SNP 1859460 G A scaffold49652_1861379_SNP 1861379 A C scaffold49652_1861990_SNP 1861990 T C scaffold49652_1862056_SNP 1862056 G C scaffold49652_1862087_SNP 1862087 C A scaffold49652_1880564_SNP 1880564 T C scaffold49652_1882681_SNP 1882681 A T scaffold49652_1884227_SNP 1884227 G A scaffold49652_1889340_SNP 1889340 C A scaffold49652_1894466_SNP 1894466 A C scaffold49652_1894728_SNP 1894728 A G scaffold49652_1895837_SNP 1895837 C T scaffold49652_1896550_SNP 1896550 T G scaffold49652_1897010_SNP 1897010 C T scaffold49652_1899601_SNP 1899601 T A scaffold49652_1914992_SNP 1914992 T A scaffold49652_1929057_SNP 1929057 G A scaffold49652_1947534_SNP 1947534 A T scaffold49652_1950635_SNP 1950635 G A scaffold49652_1952814_SNP 1952814 C T scaffold49652_1952944_SNP 1952944 A G scaffold49652_1955067_SNP 1955067 G T scaffold49652_1955972_SNP 1955972 A C scaffold49652_1957208_SNP 1957208 T G scaffold49652_1957376_SNP 1957376 A G scaffold49652_1957591_SNP 1957591 C T scaffold49652_1957619_SNP 1957619 T C scaffold49652_1957630_SNP 1957630 G T scaffold49652_1969812_SNP 1969812 A C scaffold49652_1970984_SNP 1970984 T C scaffold49652_1973861_SNP 1973861 T C scaffold49652_1975056_SNP 1975056 T G scaffold49652_1993051_SNP 1993051 A G scaffold49652_1994772_SNP 1994772 G A scaffold49652_1994940_SNP 1994940 A G scaffold49652_1995121_SNP 1995121 G A scaffold49652_1996301_SNP 1996301 A G scaffold49652_1996348_SNP 1996348 A G scaffold49652_2002224_SNP 2002224 T G scaffold49652_2002613_SNP 2002613 C A scaffold49652_2007617_SNP 2007617 T C scaffold49652_2010119_SNP 2010119 A G scaffold49652_2010941_SNP 2010941 G A scaffold49652_2012896_SNP 2012896 C T scaffold49652_2019626_SNP 2019626 T C scaffold49652_2020758_SNP 2020758 C T scaffold49652_2021039_SNP 2021039 T C scaffold49652_2021994_SNP 2021994 C T scaffold49652_2031624_SNP 2031624 G T scaffold49652_2059291_SNP 2059291 G A scaffold49652_2064077_SNP 2064077 C T scaffold49652_2068668_SNP 2068668 T C scaffold49652_2075781_SNP 2075781 C T scaffold49652_2076365_SNP 2076365 C T scaffold49652_2076469_SNP 2076469 T C scaffold49652_2092527_SNP 2092527 T C scaffold49652_2092549_SNP 2092549 T C scaffold49652_2092809_SNP 2092809 C G scaffold49652_2094093_SNP 2094093 C A scaffold49652_2105568_SNP 2105568 A G scaffold49652_2115691_SNP 2115691 T A scaffold49652_2125447_SNP 2125447 C T scaffold49652_2126155_SNP 2126155 G A scaffold49652_2133188_SNP 2133188 T C scaffold49652_2138716_SNP 2138716 T C scaffold49652_2138774_SNP 2138774 T C scaffold49652_2156405_SNP 2156405 G C scaffold49652_2161240_SNP 2161240 C T scaffold49652_2178581_SNP 2178581 C G scaffold49652_2185469_SNP 2185469 A T scaffold49652_2187968_SNP 2187968 T C scaffold49652_2188098_SNP 2188098 T C scaffold49652_2188172_SNP 2188172 C T scaffold49652_2188805_SNP 2188805 G C scaffold49652_2198605_SNP 2198605 G A scaffold49652_2201366_SNP 2201366 A C scaffold49652_2216007_SNP 2216007 C T scaffold49652_2216622_SNP 2216622 G A scaffold49652_2227103_SNP 2227103 T G scaffold49652_2252002_SNP 2252002 A C scaffold49652_2267719_SNP 2267719 G T scaffold49652_2267778_SNP 2267778 G C scaffold49652_2275369_SNP 2275369 A T scaffold49652_2278763_SNP 2278763 A G scaffold49652_2284434_SNP 2284434 G T scaffold49652_2289155_SNP 2289155 G A scaffold49652_2293585_SNP 2293585 G A scaffold49652_2295350_SNP 2295350 A G scaffold49652_2319323_SNP 2319323 A T scaffold49652_2319892_SNP 2319892 A G scaffold49652_2340651_SNP 2340651 G C scaffold49652_2342022_SNP 2342022 G T scaffold49652_2350721_SNP 2350721 C A scaffold49652_2353391_SNP 2353391 T G scaffold49652_2368805_SNP 2368805 A G scaffold49652_2380689_SNP 2380689 T C scaffold49652_2380714_SNP 2380714 A C scaffold49652_2382130_SNP 2382130 T C scaffold49652_2383282_SNP 2383282 C T scaffold49652_2383554_SNP 2383554 T C scaffold49652_2384963_SNP 2384963 C T scaffold49652_2387325_SNP 2387325 C T scaffold49652_2387645_SNP 2387645 G A scaffold49652_2388437_SNP 2388437 A C scaffold49652_2400554_SNP 2400554 T G scaffold49652_2402164_SNP 2402164 T C scaffold49652_2405435_SNP 2405435 A G scaffold49652_2409799_SNP 2409799 C T scaffold49652_2410701_SNP 2410701 C T scaffold49652_2415748_SNP 2415748 A G scaffold49652_2415764_SNP 2415764 T C scaffold49652_2422192_SNP 2422192 T G scaffold49652_2442690_SNP 2442690 A G scaffold49652_2444153_SNP 2444153 A C scaffold49652_2458358_SNP 2458358 G T scaffold49652_2460701_SNP 2460701 G C scaffold49652_2471976_SNP 2471976 T A scaffold49652_2475982_SNP 2475982 G C scaffold49652_2476211_SNP 2476211 A C scaffold49652_2483904_SNP 2483904 C A scaffold49652_2492670_SNP 2492670 G T scaffold49652_2492681_SNP 2492681 C T scaffold49652_2503387_SNP 2503387 A G scaffold49652_2512568_SNP 2512568 C A scaffold49652_2513576_SNP 2513576 C A

TABLE 3 SNP Positions within SEQ ID NO: 3 that are associated with increased resistance to ASR Favorable Unfavorable Allele (Rust Allele (Rust SNP Name Position Resistant) Susceptible) 002687F_347209_SNP||S_164680479 347209 C T 002687F_205199_SNP||S_164660488 205199 A C 002687F_219471_SNP||S_164662254 219471 A T 002687F_219766_SNP||S_164662304 219766 A C 002687F_342670_SNP||S_164679830 342670 T A 002687F_347216_SNP||S_164680481 347216 C T 002687F_214317_SNP||S_164661625 214317 G T 002687F_214627_SNP||S_164661653 214627 T A 002687F_214883_SNP||S_164661676 214883 T C 002687F_223183_SNP||S_164662750 223183 C T 002687F_224184_SNP||S_164662864 224184 T G 002687F_224879_SNP||S_164662947 224879 T C 002687F_347638_SNP||S_164680535 347638 G A 002687F_213909_SNP||S_164661595 213909 C A 002687F_342685_SNP||S_164679832 342685 A C 002687F_355543_SNP||S_164681678 355543 G A 002687F_220657_SNP||S_164662418 220657 A G 002687F_208869_SNP||S_164661018 208869 G A 002687F_220760_SNP||S_164662425 220760 C A 002687F_221002_SNP||S_164662446 221002 G A 002687F_279573_SNP||S_164670418 279573 C G 002687F_215594_SNP||S_164661771 215594 T C 002687F_236335_SNP||S_164664304 236335 T C 002687F_213017_SNP||S_164661504 213017 T G 002687F_220051_SNP||S_164662335 220051 A T 002687F_4944_SNP||S_164619728 4944 T C 002687F_343869_SNP||S_164679986 343869 T A 002687F_227603_SNP||S_164663273 227603 A G 002687F_200922_SNP||S_164659943 200922 C T 002687F_202410_SNP||S_164660103 202410 T C 002687F_257232_SNP||S_164667413 257232 C T 002687F_258539_SNP||S_164667602 258539 A C 002687F_264907_SNP||S_164668587 264907 T A 002687F_265651_SNP||S_164668676 265651 C T 002687F_271932_SNP||S_164669551 271932 T C 002687F_283205_SNP||S_164670839 283205 C T 002687F_204093_SNP||S_164660340 204093 C T 002687F_210615_SNP 210615 T C 002687F_237462_SNP||S_164664507 237462 T A 002687F_244322_SNP||S_164665473 244322 G C 002687F_262053_SNP||S_164668143 262053 C T 002687F_236247_SNP||S_164664292 236247 C T 002687F_236323_SNP||S_164664301 236323 T C 002687F_154489_SNP||S_164653160 154489 A G 002687F_233977_SNP||S_164664019 233977 A G 002687F_257999_SNP||S_164667512 257999 G A 002687F_279277_SNP||S_164670387 279277 A G 002687F_282755_SNP||S_164670788 282755 G A 002687F_283768_SNP||S_164670937 283768 T C 002687F_302554_SNP||S_164673590 302554 A G 002687F_164869_SNP||S_164655174 164869 T G 002687F_288304_SNP||S_164671605 288304 T G 002687F_294526_SNP||S_164672282 294526 T G 002687F_309973_SNP||S_164674519 309973 G T 002687F_337382_SNP||S_164679163 337382 G A 002687F_211731_SNP||S_164661365 211731 C T 002687F_220577_SNP||S_164662407 220577 G A 002687F_237097_SNP||S_164664465 237097 T C 002687F_266479_SNP||S_164668817 266479 C A 002687F_271386_SNP||S_164669455 271386 T G 002687F_273756_SNP||S_164669758 273756 C T 002687F_273817_SNP||S_164669764 273817 T C 002687F_276363_SNP||S_164670071 276363 G A 002687F_298340_SNP||S_164672831 298340 G A 002687F_238876_SNP||S_164664664 238876 T A 002687F_239424_SNP||S_164664741 239424 A G 002687F_256831_SNP||S_164667336 256831 G A 002687F_259186_SNP||S_164667703 259186 A G 002687F_275640_SNP||S_164669976 275640 G A 002687F_277720_SNP||S_164670211 277720 T C 002687F_279232_SNP||S_164670381 279232 C T 002687F_263744_SNP||S_164668442 263744 T A 002687F_304142_SNP||S_164673806 304142 A G 002687F_281179_SNP||S_164670589 281179 G A 002687F_236591_SNP||S_164664403 236591 G A 002687F_297512_SNP||S_164672702 297512 A T 002687F_305090_SNP||S_164673953 305090 T A 002687F_224674_SNP||S_164662923 224674 A G 002687F_275330_SNP||S_164669940 275330 A G 002687F_304685_SNP 304685 T G 002687F_319681_SNP 319681 T C 002687F_353495_SNP 353495 C T 002687F_52497_SNP||S_164627583 52497 T C 002687F_268767_SNP 268767 G C 002687F_278674_SNP 278674 A G 002687F_302719_SNP 302719 T C 002687F_343777_SNP 343777 T C 002687F_168567_SNP||S_164655687 168567 A T 002687F_325074_SNP||S_164677221 325074 T G 002687F_325106_SNP||S_164677230 325106 T C 002687F_333863_SNP 333863 A G 002687F_195487_SNP 195487 A T 002687F_228040_SNP||S_164663308 228040 T A 002687F_244345_SNP 244345 T A 002687F_278494_SNP||S_164670290 278494 A G 002687F_349619_SNP 349619 C T 002687F_198468_SNP 198468 G T 002687F_224844_SNP 224844 A G 002687F_224922_SNP 224922 A G 002687F_275515_SNP 275515 T A 002687F_292027_SNP 292027 T A 002687F_346308_SNP 346308 T C 002687F_362288_SNP 362288 A C 002687F_185377_SNP 185377 G A 002687F_220542_SNP 220542 G A 002687F_223788_SNP 223788 A T 002687F_343709_SNP 343709 T C 002687F_343862_SNP 343862 A G 002687F_201858_SNP 201858 T G 002687F_333763_SNP 333763 A G 002687F_347210_SNP 347210 A G 002687F_160730_SNP 160730 A G 002687F_161496_SNP 161496 A G 002687F_189663_SNP 189663 C T 002687F_341508_SNP 341508 A T 002687F_346605_SNP 346605 A G 002687F_362101_SNP 362101 G A

TABLE 4 SNP Positions within SEQ ID NO: 4 that are associated with increased resistance to ASR Favorable Unfavorable Allele (Rust Allele (Rust SNP Name Position Resistant) Susceptible) 001084F-001-01_1285_SNP||S_96261695 1285 T A 001084F-001-01_1521_SNP||S_96261716 1521 C A 001084F-001-01_2588_SNP||S_96261833 2588 A G 001084F-001-01_2699_SNP||S_96261849 2699 G A 001084F-001-01_7021_SNP||S_96262358 7021 T C 001084F-001-01_8184_SNP||S_96262509 8184 G A 001084F-001-01_9147_SNP||S_96262590 9147 G T 001084F-001-01_10435_SNP||S_96262737 10435 G C 001084F-001-01_13118_SNP||S_96263136 13118 C T 001084F_27070_SNP||S_96182069 27070 T C 001084F_28184_SNP||S_96182234 28184 G T 001084F_31379_SNP||S_96182641 31379 C G 001084F_32184_SNP||S_96182765 32184 C T 001084F_42660_SNP||S_96183942 42660 T A 001084F_52001_SNP||S_96185095 52001 C T 001084F_52023_SNP 52023 A G 001084F_57467_SNP||S_96185758 57467 A C 001084F_57737_SNP||S_96185798 57737 C G 001084F_58089_SNP||S_96185849 58089 G A 001084F_63976_SNP||S_96186652 63976 G A 001084F_65903_SNP||S_96186876 65903 A G 001084F_82007_SNP||S_96188830 82007 G T 001084F-001-01_82274_SNP||S_96272178 82274 T G 001084F_84479_SNP||S_96189187 84479 T G 001084F_85287_SNP||S_96189334 85287 A C 001084F_85888_SNP||S_96189417 85888 A T 001084F_86201_SNP||S_96189465 86201 C T 001084F-001-01_86502_SNP||S_96272667 86502 A G 001084F_87914_SNP||S_96189697 87914 G A 001084F_88555_SNP||S_96189801 88555 T A 001084F_93651_SNP||S_96190428 93651 G A 001084F_95283_SNP||S_96190621 95283 G C 001084F-001-01_97554_SNP||S_96274217 97554 A C 001084F_98814_SNP||S_96191018 98814 C A 001084F_103767_SNP||S_96191744 103767 T A 001084F_106721_SNP||S_96192163 106721 G T 001084F_110421_SNP||S_96192646 110421 C G 001084F_111143_SNP||S_96192765 111143 C T 001084F_111365_SNP||S_96192803 111365 A G 001084F_113202_SNP||S_96193055 113202 A T 001084F_114276_SNP 114276 G T 001084F_114340_SNP||S_96193207 114340 A G 001084F_114450_SNP||S_96193224 114450 T C 001084F_114536_SNP||S_96193238 114536 G A 001084F_115661_SNP||S_96193442 115661 T C 001084F_121396_SNP||S_96194243 121396 A T 001084F_122184_SNP||S_96194326 122184 A G 001084F_123018_SNP||S_96194413 123018 T C 001084F_123034_SNP||S_96194416 123034 A T 001084F_124257_SNP||S_96194591 124257 A C 001084F_124583_SNP||S_96194626 124583 G A 001084F_125117_SNP||S_96194736 125117 C A 001084F_125329_SNP||S_96194763 125329 C G 001084F_125691_SNP||S_96194803 125691 T C 001084F_126047_SNP||S_96194860 126047 A T 001084F_126132_SNP||S_96194877 126132 G A 001084F_126350_SNP 126350 A G 001084F_126379_SNP||S_96194890 126379 G A 001084F_126664_SNP||S_96194933 126664 A G 001084F_126712_SNP||S_96194939 126712 G C 001084F-001-01_127911_SNP||S_96278033 127911 C T 001084F_129197_SNP||S_96195328 129197 A G 001084F_129484_SNP||S_96195378 129484 T C 001084F_130167_SNP||S_96195529 130167 C T 001084F_130305_SNP||S_96195546 130305 A G 001084F_130497_SNP||S_96195566 130497 C A 001084F_130604_SNP 130604 A C 001084F_132646_SNP||S_96195748 132646 A C 001084F_132795_SNP||S_96195769 132795 A C 001084F_133258_SNP||S_96195812 133258 A C 001084F_133487_SNP||S_96195836 133487 T A 001084F_139504_SNP||S_96195994 139504 T C 001084F_140393_SNP||S_96196060 140393 G A 001084F_140734_SNP||S_96196116 140734 G A 001084F_140889_SNP||S_96196121 140889 G A 001084F_140943_SNP||S_96196125 140943 C G 001084F_140956_SNP||S_96196127 140956 T C 001084F_141136_SNP||S_96196151 141136 C T 001084F_141999_SNP||S_96196230 141999 A T 001084F_142002_SNP||S_96196231 142002 T C 001084F_142266_SNP||S_96196269 142266 G A 001084F_142328_SNP||S_96196272 142328 A G 001084F_142364_SNP||S_96196276 142364 A T 001084F_142627_SNP 142627 T C 001084F_142993_SNP||S_96196324 142993 A C 001084F_143091_SNP||S_96196333 143091 A T 001084F_143145_SNP||S_96196341 143145 T C 001084F_143227_SNP||S_96196350 143227 A C 001084F_143257_SNP||S_96196353 143257 A G 001084F_144001_SNP||S_96196414 144001 A C 001084F_144670_SNP||S_96196479 144670 A G 001084F_144689_SNP||S_96196480 144689 G A 001084F_144794_SNP||S_96196492 144794 A C 001084F_145076_SNP 145076 C T 001084F_147040_SNP||S_96196783 147040 G T 001084F_148598_SNP||S_96196947 148598 G A 001084F_150856_SNP||S_96197142 150856 G A 001084F_150890_SNP||S_96197144 150890 C T 001084F_150946_SNP||S_96197148 150946 C G 001084F_151501_SNP||S_96197186 151501 C T 001084F_151988_SNP||S_96197248 151988 G T 001084F_152716_SNP||S_96197335 152716 A C 001084F_152718_SNP||S_96197336 152718 G A 001084F_153080_SNP||S_96197385 153080 G T 001084F_154824_SNP||S_96197620 154824 T A 001084F_155266_SNP||S_96197675 155266 A T 001084F_156572_SNP||S_96197878 156572 G A 001084F_157730_SNP||S_96198007 157730 T C 001084F_158682_SNP||S_96198187 158682 T C 001084F_158723_SNP||S_96198192 158723 T G 001084F_158742_SNP||S_96198194 158742 G A 001084F_159166_SNP||S_96198257 159166 A T 001084F_159313_SNP||S_96198276 159313 A G 001084F_159442_SNP||S_96198291 159442 C T 001084F_159587_SNP||S_96198308 159587 T C 001084F_160320_SNP||S_96198404 160320 A C 001084F_160645_SNP||S_96198429 160645 T C 001084F_161095_SNP||S_96198508 161095 C T 001084F_161709_SNP||S_96198644 161709 C T 001084F_162179_SNP||S_96198670 162179 C G 001084F_162814_SNP||S_96198732 162814 A T 001084F_163017_SNP||S_96198749 163017 C A 001084F_163383_SNP||S_96198774 163383 G T 001084F_163680_SNP||S_96198808 163680 G A 001084F_164905_SNP||S_96198896 164905 C A 001084F_167287_SNP||S_96199111 167287 G T 001084F_167515_SNP||S_96199122 167515 G C 001084F_167652_SNP||S_96199135 167652 T C 001084F_167962_SNP||S_96199157 167962 A T 001084F_168247_SNP||S_96199187 168247 T A 001084F_168725_SNP||S_96199246 168725 A G 001084F_168757_SNP||S_96199252 168757 C T 001084F_169076_SNP||S_96199300 169076 A G 001084F_169079_SNP||S_96199301 169079 C T 001084F_169225_SNP||S_96199313 169225 T C 001084F_169491_SNP||S_96199351 169491 A G 001084F_169747_SNP||S_96199380 169747 G T 001084F_170170_SNP||S_96199415 170170 A G 001084F_170426_SNP||S_96199442 170426 A T 001084F_170606_SNP||S_96199460 170606 A C 001084F_170818_SNP||S_96199484 170818 T G 001084F_171563_SNP||S_96199521 171563 A G 001084F_172571_SNP||S_96199666 172571 G T 001084F_172598_SNP||S_96199673 172598 G C 001084F_172978_SNP||S_96199717 172978 A G 001084F_173956_SNP||S_96199838 173956 C T 001084F_174469_SNP||S_96199929 174469 T G 001084F_174541_SNP||S_96199946 174541 G C 001084F_174758_SNP||S_96199978 174758 C T 001084F_174810_SNP||S_96199982 174810 C G 001084F_175992_SNP||S_96200176 175992 A T 001084F_176004_SNP||S_96200178 176004 G A 001084F_176028_SNP||S_96200179 176028 A G 001084F_176079_SNP||S_96200184 176079 G A 001084F_176112_SNP||S_96200191 176112 T C 001084F_176675_SNP||S_96200247 176675 C T 001084F_176780_SNP||S_96200251 176780 A G 001084F_176983_SNP||S_96200275 176983 A T 001084F_177786_SNP||S_96200387 177786 C A 001084F_177903_SNP||S_96200440 177903 G A 001084F_177935_SNP||S_96200455 177935 G A 001084F_178018_SNP||S_96200464 178018 A T 001084F_178034_SNP||S_96200468 178034 C A 001084F_178300_SNP||S_96200512 178300 C G 001084F_178555_SNP||S_96200539 178555 A G 001084F_178630_SNP||S_96200546 178630 G A 001084F_179301_SNP||S_96200625 179301 A T 001084F_179344_SNP||S_96200632 179344 C T 001084F_179983_SNP||S_96200681 179983 C T 001084F_179991_SNP||S_96200682 179991 C T 001084F_179996_SNP||S_96200683 179996 C A 001084F_180047_SNP||S_96200686 180047 C G 001084F_180211_SNP 180211 A T 001084F_180253_SNP||S_96200700 180253 A G 001084F_180363_SNP||S_96200718 180363 A G 001084F_181550_SNP||S_96200860 181550 A C 001084F_184764_SNP||S_96201129 184764 C A 001084F_185504_SNP||S_96201216 185504 G A 001084F_185881_SNP||S_96201245 185881 T C 001084F_185892_SNP||S_96201246 185892 A T 001084F_186629_SNP||S_96201304 186629 A G 001084F_188635_SNP||S_96201526 188635 A G 001084F_190570_SNP||S_96201789 190570 T C 001084F_198311_SNP||S_96202837 198311 A T 001084F_199171_SNP||S_96202922 199171 G A 001084F_202466_SNP||S_96203367 202466 T C 001084F_205193_SNP||S_96203796 205193 T A 001084F_211317_SNP||S_96204657 211317 A T 001084F_213117_SNP||S_96204953 213117 T C 001084F_213481_SNP||S_96205009 213481 T C 001084F_213587_SNP||S_96205028 213587 G T 001084F_218631_SNP||S_96205568 218631 G A 001084F_226564_SNP||S_96206645 226564 C T 001084F_227857_SNP||S_96206816 227857 G A 001084F_237891_SNP||S_96208029 237891 A C 001084F_239017_SNP||S_96208161 239017 C T 001084F_239368_SNP||S_96208190 239368 T G 001084F_239536_SNP||S_96208211 239536 C T 001084F_239682_SNP||S_96208242 239682 T A 001084F_245799_SNP||S_96209112 245799 A T 001084F_246318_SNP||S_96209151 246318 C T 001084F_246386_SNP||S_96209159 246386 A T 001084F_249008_SNP||S_96209600 249008 A G 001084F_250639_SNP 250639 T C 001084F_250641_SNP 250641 C T 001084F_251193_SNP||S_96209831 251193 T C 001084F_251515_SNP||S_96209892 251515 A G 001084F_252366_SNP||S_96209966 252366 T C 001084F_252578_SNP||S_96209979 252578 C G 001084F_253950_SNP||S_96210134 253950 C G 001084F_253956_SNP||S_96210135 253956 G A 001084F_254157_SNP||S_96210146 254157 T G 001084F_254286_SNP||S_96210168 254286 G T 001084F_254514_SNP||S_96210191 254514 A G 001084F_254545_SNP||S_96210194 254545 A G 001084F_255300_SNP||S_96210279 255300 G C 001084F_255476_SNP||S_96210306 255476 C T 001084F_255933_SNP||S_96210349 255933 C T 001084F_255992_SNP||S_96210355 255992 G A 001084F_256289_SNP||S_96210412 256289 C T 001084F_256296_SNP||S_96210413 256296 A G 001084F_256670_SNP||S_96210467 256670 T A 001084F_256861_SNP||S_96210477 256861 T C 001084F_256888_SNP||S_96210478 256888 T G 001084F_256929_SNP||S_96210482 256929 G A 001084F_257126_SNP||S_96210501 257126 C T 001084F_257133_SNP||S_96210503 257133 T C 001084F_257136_SNP||S_96210504 257136 T C 001084F_257289_SNP||S_96210519 257289 T C 001084F_257327_SNP||S_96210520 257327 A G 001084F_257534_SNP||S_96210589 257534 G C 001084F_257676_SNP||S_96210618 257676 C T 001084F_257874_SNP||S_96210661 257874 C G 001084F_257934_SNP||S_96210667 257934 G A 001084F_258230_SNP||S_96210699 258230 C G 001084F_258395_SNP||S_96210734 258395 C G 001084F_258418_SNP||S_96210739 258418 G T 001084F_258653_SNP||S_96210766 258653 A G 001084F_259060_SNP||S_96210844 259060 C A 001084F_259168_SNP 259168 G T 001084F_259273_SNP||S_96210882 259273 A G 001084F_259443_SNP||S_96210898 259443 C G 001084F_260067_SNP||S_96210964 260067 C T 001084F_260664_SNP||S_96211072 260664 T C 001084F_261242_SNP||S_96211105 261242 G A 001084F_262054_SNP||S_96211201 262054 G A 001084F_262740_SNP||S_96211245 262740 C A 001084F_263131_SNP||S_96211295 263131 C T 001084F_263585_SNP||S_96211367 263585 A C 001084F_263650_SNP||S_96211378 263650 G A 001084F_263970_SNP||S_96211410 263970 T C 001084F_264720_SNP||S_96211554 264720 A T 001084F_265298_SNP||S_96211619 265298 A C 001084F_265844_SNP||S_96211678 265844 C T 001084F_265895_SNP||S_96211683 265895 A G 001084F_268195_SNP||S_96211902 268195 T G 001084F_270197_SNP||S_96212223 270197 G A 001084F_271842_SNP||S_96212410 271842 A G 001084F_272342_SNP||S_96212494 272342 T C 001084F_272520_SNP||S_96212517 272520 C T 001084F_273104_SNP||S_96212595 273104 C A 001084F_273591_SNP||S_96212652 273591 T C 001084F_273652_SNP||S_96212656 273652 A C 001084F_275546_SNP||S_96212833 275546 T C 001084F_275658_SNP||S_96212859 275658 T A 001084F_278078_SNP||S_96213204 278078 G A 001084F_279158_SNP||S_96213320 279158 A C 001084F_279575_SNP||S_96213380 279575 A G 001084F_279729_SNP||S_96213387 279729 C G 001084F_279954_SNP||S_96213419 279954 C T 001084F_281389_SNP||S_96213625 281389 C T 001084F_281513_SNP||S_96213642 281513 C T 001084F_281542_SNP||S_96213648 281542 C T 001084F_285388_SNP||S_96214072 285388 C T 001084F_285487_SNP||S_96214096 285487 C T 001084F_285683_SNP||S_96214122 285683 C T 001084F_285771_SNP||S_96214134 285771 G T 001084F_286094_SNP||S_96214209 286094 A G 001084F_286116_SNP||S_96214211 286116 A G 001084F_288436_SNP||S_96214424 288436 A T 001084F_292939_SNP||S_96215141 292939 G C 001084F_293422_SNP||S_96215191 293422 C T 001084F_293810_SNP||S_96215229 293810 A G 001084F_295524_SNP||S_96215424 295524 A G 001084F_299778_SNP||S_96215969 299778 A G 001084F_299821_SNP||S_96215974 299821 G T 001084F_300075_SNP||S_96215990 300075 G A 001084F_300887_SNP||S_96216153 300887 A G 001084F_301156_SNP||S_96216230 301156 G A 001084F_301165_SNP||S_96216235 301165 T C 001084F_301641_SNP||S_96216305 301641 A G 001084F_301793_SNP||S_96216321 301793 A C 001084F_301853_SNP||S_96216333 301853 C T 001084F_302997_SNP 302997 C T 001084F_303003_SNP 303003 C T 001084F_304597_SNP||S_96216721 304597 G A 001084F_304622_SNP||S_96216723 304622 T C 001084F_304909_SNP||S_96216751 304909 T C 001084F_305891_SNP||S_96216891 305891 G A 001084F_306716_SNP||S_96217046 306716 G A 001084F_307693_SNP 307693 G A 001084F_310749_SNP||S_96217542 310749 C T 001084F_313646_SNP||S_96217955 313646 A T 001084F_313895_SNP||S_96217991 313895 A G 001084F_314482_SNP||S_96218079 314482 G T 001084F_315263_SNP||S_96218215 315263 G A 001084F_315605_SNP||S_96218253 315605 C A 001084F_316003_SNP||S_96218288 316003 C A 001084F_325995_SNP||S_96219601 325995 T G 001084F_326011_SNP||S_96219606 326011 A G 001084F_326714_SNP||S_96219700 326714 C T 001084F_327975_SNP||S_96219824 327975 T A 001084F_333039_SNP||S_96220391 333039 T C 001084F_335872_SNP||S_96220742 335872 A G 001084F_336344_SNP||S_96220819 336344 G T 001084F_337412_SNP||S_96220956 337412 C T 001084F_344980_SNP||S_96221826 344980 A C 001084F_345034_SNP||S_96221832 345034 T G 001084F_346595_SNP 346595 T G 001084F_346779_SNP 346779 T C 001084F_366657_SNP||S_96224390 366657 C A 001084F_368696_SNP||S_96224623 368696 A G 001084F_370079_SNP||S_96224756 370079 A G 001084F_370253_SNP||S_96224774 370253 T C 001084F_380989_SNP||S_96226270 380989 A G 001084F_382368_SNP||S_96226437 382368 C T 001084F_386547_SNP||S_96226875 386547 C T 001084F_392211_SNP||S_96227525 392211 C T 001084F_392954_SNP 392954 G C 001084F_393013_SNP||S_96227637 393013 T C 001084F_393748_SNP||S_96227753 393748 T C 001084F_394557_SNP||S_96227856 394557 G A 001084F_395656_SNP||S_96228004 395656 A G 001084F_395876_SNP||S_96228023 395876 T A 001084F_397385_SNP||S_96228189 397385 G T 001084F_398551_SNP||S_96228339 398551 C T 001084F_404731_SNP||S_96229018 404731 A G 001084F_404792_SNP||S_96229021 404792 T A 001084F_405196_SNP||S_96229072 405196 C T 001084F_405197_SNP||S_96229073 405197 A C 001084F_405198_SNP||S_96229074 405198 T A 001084F_405731_SNP||S_96229143 405731 C G 001084F_407194_SNP||S_96229325 407194 A G 001084F_409622_SNP||S_96229641 409622 A T 001084F_410452_SNP||S_96229734 410452 C T 001084F_412571_SNP||S_96229970 412571 T C 001084F_412785_SNP||S_96230001 412785 A G 001084F_413752_SNP||S_96230139 413752 G A 001084F_416185_SNP||S_96230412 416185 G T 001084F_416395_SNP||S_96230427 416395 C A 001084F_416591_SNP||S_96230446 416591 T G 001084F_416593_SNP||S_96230447 416593 G C 001084F_417106_SNP||S_96230492 417106 G C 001084F_419325_SNP||S_96230786 419325 A G 001084F_419460_SNP||S_96230801 419460 C A 001084F_420529_SNP||S_96230939 420529 C T 001084F_420584_SNP||S_96230944 420584 A G 001084F_421121_SNP||S_96231014 421121 T C 001084F_427016_SNP||S_96231729 427016 G C 001084F_432148_SNP||S_96232338 432148 A G 001084F_432700_SNP||S_96232398 432700 A G 001084F_432798_SNP||S_96232404 432798 A G 001084F_433511_SNP||S_96232528 433511 C T 001084F_433994_SNP||S_96232606 433994 T A 001084F_434231_SNP||S_96232644 434231 G T 001084F_436588_SNP||S_96232887 436588 A G 001084F_437273_SNP||S_96232934 437273 T C 001084F_439876_SNP||S_96233294 439876 T G 001084F_446565_SNP||S_96234158 446565 C A 001084F_446712_SNP||S_96234176 446712 A G 001084F_446950_SNP||S_96234212 446950 C T 001084F_448070_SNP||S_96234319 448070 T C 001084F_448364_SNP||S_96234350 448364 C T 001084F_449012_SNP 449012 A G 001084F_449590_SNP||S_96234450 449590 C T 001084F_451682_SNP||S_96234684 451682 T C 001084F_453264_SNP 453264 A G 001084F_454594_SNP||S_96235135 454594 G A 001084F_457770_SNP||S_96235545 457770 T C 001084F_458788_SNP||S_96235648 458788 A G 001084F_459147_SNP||S_96235687 459147 C T 001084F_461166_SNP||S_96236019 461166 A G 001084F_461247_SNP||S_96236039 461247 G A 001084F_461752_SNP||S_96236125 461752 C T 001084F_466437_SNP||S_96236630 466437 T G 001084F_466805_SNP||S_96236678 466805 T C 001084F_467644_SNP||S_96236780 467644 A C 001084F_468704_SNP||S_96236898 468704 T A 001084F_471659_SNP||S_96237333 471659 T A 001084F_471667_SNP||S_96237334 471667 G T 001084F_471959_SNP||S_96237354 471959 T G 001084F_474765_SNP||S_96237787 474765 T C 001084F_475731_SNP||S_96237878 475731 A T 001084F_476014_SNP||S_96237900 476014 A T 001084F_481574_SNP||S_96238618 481574 C T 001084F_481748_SNP||S_96238640 481748 A T 001084F_481949_SNP||S_96238661 481949 T A 001084F_483822_SNP||S_96238932 483822 C T 001084F_483922_SNP||S_96238940 483922 A C 001084F_491255_SNP||S_96239840 491255 T C 001084F_491264_SNP||S_96239843 491264 C T 001084F_491333_SNP||S_96239854 491333 A G 001084F_491388_SNP||S_96239874 491388 C T 001084F_491438_SNP||S_96239884 491438 C A 001084F_491456_SNP||S_96239888 491456 T C 001084F_491474_SNP||S_96239891 491474 A G 001084F_492676_SNP||S_96240013 492676 C G 001084F_492681_SNP||S_96240014 492681 C T 001084F_493223_SNP||S_96240071 493223 G A 001084F_493257_SNP||S_96240074 493257 C T 001084F_495167_SNP||S_96240310 495167 G T 001084F_495237_SNP||S_96240320 495237 A G 001084F_496103_SNP 496103 C A 001084F_511172_SNP||S_96242515 511172 T C 001084F_575347_SNP||S_96250573 575347 A G 001084F_577730_SNP||S_96251010 577730 G A 001084F_578149_SNP||S_96251054 578149 G A 001084F_579372_SNP||S_96251212 579372 A G 001084F_586316_SNP||S_96252046 586316 A G 001084F_589859_SNP||S_96252610 589859 T C 001084F_589957_SNP||S_96252616 589957 T C 001084F_589968_SNP||S_96252619 589968 T C 001084F_590712_SNP||S_96252758 590712 T C 001084F_591010_SNP||S_96252775 591010 T A 001084F_591944_SNP||S_96252903 591944 C A 001084F_592110_SNP||S_96252917 592110 C T 001084F_592173_SNP||S_96252923 592173 G A 001084F_594029_SNP||S_96253180 594029 A G 001084F_594234_SNP||S_96253198 594234 T C 001084F_594408_SNP||S_96253219 594408 C T 001084F_594539_SNP||S_96253244 594539 G A 001084F_595688_SNP||S_96253403 595688 C T 001084F_595748_SNP||S_96253409 595748 A G 001084F_596093_SNP||S_96253455 596093 A C 001084F_598845_SNP||S_96253843 598845 G A 001084F_599340_SNP||S_96253911 599340 A C 001084F_600996_SNP||S_96254147 600996 A G 001084F_601300_SNP||S_96254185 601300 T C 001084F_601957_SNP||S_96254250 601957 G A 001084F_602486_SNP 602486 C T 001084F_606403_SNP||S_96254906 606403 C G 001084F_607071_SNP||S_96254986 607071 G T 001084F_610092_SNP||S_96255394 610092 T C 001084F_610896_SNP||S_96255567 610896 A G 001084F_611678_SNP||S_96255725 611678 C T 001084F_612116_SNP||S_96255826 612116 C T 001084F_613144_SNP||S_96256025 613144 A G 001084F_614025_SNP 614025 G A 001084F_616919_SNP||S_96256727 616919 T G 001084F_617682_SNP||S_96256806 617682 A T 001084F_617849_SNP||S_96256827 617849 A G 001084F_618353_SNP 618353 T C 001084F_621278_SNP||S_96257215 621278 G T 001084F_621394_SNP||S_96257226 621394 T C 001084F_623147_SNP||S_96257479 623147 A G 001084F_624529_SNP 624529 T A 001084F_627999_SNP||S_96258130 627999 T G 001084F_628120_SNP||S_96258147 628120 C T 001084F_628359_SNP||S_96258172 628359 T G 001084F_628992_SNP||S_96258268 628992 T C 001084F_629050_SNP||S_96258285 629050 A G 001084F_629328_SNP||S_96258334 629328 C T 001084F_630582_SNP||S_96258523 630582 G C 001084F_631413_SNP||S_96258645 631413 T G 001084F_633048_SNP||S_96258882 633048 A T 001084F_643660_SNP||S_96261113 643660 A G

TABLE 5 SNP Positions within SEQ ID NO: 5 that are associated with increased resistance to ASR Favorable Unfavorable Allele (Rust Allele (Rust SNP Name Position Resistant) Susceptible) 000819F/G_tomentella_PI_583970_v1 114599 G C 000819F/G_tomentella_PI_583970_v1 149238 C T 000819F/G_tomentella_PI_583970_v1 149288 C T 000819F/G_tomentella_PI_583970_v1 150032 T C 000819F/G_tomentella_PI_583970_v1 151944 C T 000819F/G_tomentella_PI_583970_v1 152479 A T 000819F/G_tomentella_PI_583970_v1 155540 G A 000819F/G_tomentella_PI_583970_v1 162204 A C 000819F/G_tomentella_PI_583970_v1 163754 G A 000819F/G_tomentella_PI_583970_v1 165362 A C 000819F/G_tomentella_PI_583970_v1 165535 A T 000819F/G_tomentella_PI_583970_v1 165577 G C 000819F/G_tomentella_PI_583970_v1 167131 T C 000819F/G_tomentella_PI_583970_v1 171396 A G 000819F/G_tomentella_PI_583970_v1 172021 T C 000819F/G_tomentella_PI_583970_v1 172471 G C 000819F/G_tomentella_PI_583970_v1 177992 A C 000819F/G_tomentella_PI_583970_v1 180263 A C 000819F/G_tomentella_PI_583970_v1 181800 C T 000819F/G_tomentella_PI_583970_v1 193762 C T 000819F/G_tomentella_PI_583970_v1 194604 T A 000819F/G_tomentella_PI_583970_v1 205989 T A 000819F/G_tomentella_PI_583970_v1 212017 A G 000819F/G_tomentella_PI_583970_v1 213446 C T 000819F/G_tomentella_PI_583970_v1 232768 A T 000819F/G_tomentella_PI_583970_v1 245161 G A 000819F/G_tomentella_PI_583970_v1 245854 T A 000819F/G_tomentella_PI_583970_v1 246180 C A 000819F/G_tomentella_PI_583970_v1 246738 C T 000819F/G_tomentella_PI_583970_v1 246919 G A 000819F/G_tomentella_PI_583970_v1 248321 G A 000819F/G_tomentella_PI_583970_v1 252345 A G 000819F/G_tomentella_PI_583970_v1 252360 A T 000819F/G_tomentella_PI_583970_v1 265534 A G 000819F/G_tomentella_PI_583970_v1 266733 T C 000819F/G_tomentella_PI_583970_v1 266773 T C 000819F/G_tomentella_PI_583970_v1 266963 G A 000819F/G_tomentella_PI_583970_v1 267269 A T 000819F/G_tomentella_PI_583970_v1 267342 G A 000819F/G_tomentella_PI_583970_v1 267921 C T 000819F/G_tomentella_PI_583970_v1 267929 A G 000819F/G_tomentella_PI_583970_v1 275462 G A 000819F/G_tomentella_PI_583970_v1 275759 T C 000819F/G_tomentella_PI_583970_v1 276045 T C 000819F/G_tomentella_PI_583970_v1 276067 G A 000819F/G_tomentella_PI_583970_v1 278203 C T 000819F/G_tomentella_PI_583970_v1 278888 A T 000819F/G_tomentella_PI_583970_v1 283800 G A 000819F/G_tomentella_PI_583970_v1 284053 T A 000819F/G_tomentella_PI_583970_v1 284831 G C 000819F/G_tomentella_PI_583970_v1 287570 G C 000819F/G_tomentella_PI_583970_v1 288787 A T 000819F/G_tomentella_PI_583970_v1 289782 A T 000819F/G_tomentella_PI_583970_v1 290827 T C 000819F/G_tomentella_PI_583970_v1 291200 T C 000819F/G_tomentella_PI_583970_v1 291213 G A 000819F/G_tomentella_PI_583970_v1 293207 G A 000819F/G_tomentella_PI_583970_v1 293867 C T 000819F/G_tomentella_PI_583970_v1 297410 T G 000819F/G_tomentella_PI_583970_v1 297431 T C 000819F/G_tomentella_PI_583970_v1 297475 T C 000819F/G_tomentella_PI_583970_v1 298295 G T 000819F/G_tomentella_PI_583970_v1 298437 A G 000819F/G_tomentella_PI_583970_v1 298979 G C 000819F/G_tomentella_PI_583970_v1 303692 A G 000819F/G_tomentella_PI_583970_v1 304046 T A 000819F/G_tomentella_PI_583970_v1 304512 C T 000819F/G_tomentella_PI_583970_v1 304764 C A 000819F/G_tomentella_PI_583970_v1 305269 T C 000819F/G_tomentella_PI_583970_v1 305624 T C 000819F/G_tomentella_PI_583970_v1 306037 T A 000819F/G_tomentella_PI_583970_v1 306171 G A 000819F/G_tomentella_PI_583970_v1 318002 C T 000819F/G_tomentella_PI_583970_v1 328015 G A 000819F/G_tomentella_PI_583970_v1 333209 A G 000819F/G_tomentella_PI_583970_v1 341293 C T 000819F/G_tomentella_PI_583970_v1 344251 C T 000819F/G_tomentella_PI_583970_v1 346694 T C 000819F/G_tomentella_PI_583970_v1 347362 A C 000819F/G_tomentella_PI_583970_v1 347867 A G 000819F/G_tomentella_PI_583970_v1 369651 C A 000819F/G_tomentella_PI_583970_v1 380730 C T 000819F/G_tomentella_PI_583970_v1 381546 C T 000819F/G_tomentella_PI_583970_v1 385059 A G 000819F/G_tomentella_PI_583970_v1 386671 A T 000819F/G_tomentella_PI_583970_v1 387021 C T 000819F/G_tomentella_PI_583970_v1 387788 T A 000819F/G_tomentella_PI_583970_v1 388859 T C 000819F/G_tomentella_PI_583970_v1 401614 G C 000819F/G_tomentella_PI_583970_v1 420350 C G 000819F/G_tomentella_PI_583970_v1 427998 G A 000819F/G_tomentella_PI_583970_v1 428798 T C 000819F/G_tomentella_PI_583970_v1 450156 C T 000819F/G_tomentella_PI_583970_v1 453725 C T 000819F/G_tomentella_PI_583970_v1 466651 A G 000819F/G_tomentella_PI_583970_v1 467520 T C 000819F/G_tomentella_PI_583970_v1 501821 G A 000819F/G_tomentella_PI_583970_v1 510702 G C 000819F/G_tomentella_PI_583970_v1 533134 T G 000819F/G_tomentella_PI_583970_v1 586465 G A 000819F/G_tomentella_PI_583970_v1 704705 C G 000819F/G_tomentella_PI_583970_v1 704714 A G

Oligonucleotide primers (herein, ‘primers’) can be developed and used to identify plants carrying any one of the chromosomal intervals depicted in SEQ ID NOs 1, 2, 3, 4 and/or 5 found to be highly associated with ASR resistance. Specifically, one having ordinary skill in the art can develop primers to detect any single nucleotide polymorphism (herein ‘SNP’) as identified in any one of Tables 1-5 in respect to identifying or producing soybean lines having any one of or a portion of the chromosome intervals depicted in SEQ ID NOs: 1, 2, 3, 4 or 5 that are associated with ASR resistance. A TAQMAN® assay (e.g. generally a two-step allelic discrimination assay or similar), a KASP™ assay (generally a one-step allelic discrimination assay defined below or similar), or both can be employed to identify the SNPs that associate with increased ASR resistance as disclosed herein (e.g. favorable alleles as depicted in Tables 1-5). In an exemplary two-step assay, a forward primer, a reverse primer, and two assay probes (or hybridization oligos) are employed. The forward and reverse primers are employed to amplify genetic loci that comprise SNPs that are associated with ASR resistance loci (for example, any of the favorable alleles as shown in Tables 1-5). The particular nucleotides that are present at the SNP positions are then assayed using the assay primers (which in some embodiments are differentially labeled with, for example, fluorophores to permit distinguishing between the two assay probes in a single reaction), which in each pair differ from each other with respect to the nucleotides that are present at the SNP position (although it is noted that in any given pair, the probes can differ in their 5′ or 3′ ends without impacting their abilities to differentiate between nucleotides present at the corresponding SNP positions). In some embodiments, the assay primers and the reaction conditions are designed such that an assay primer will only hybridize to the reverse complement of a 100% perfectly matched sequence, thereby permitting identification of which allele(s) that are present based upon detection of hybridizations.

Compositions and methods for identifying, selecting and producing Glycine plants (including wild Glycines (e.g. Glycine tomentella) and Glycine max lines) with enhanced disease resistance are provided. Disease resistant soybean plants and germplasms are also provided.

In some embodiments, methods of identifying a disease resistant soybean plant or germplasm are provided. Such methods may comprise detecting, in the soybean plant or germplasm, a genetic loci or molecular marker (e.g. SNP or a Quantitative Trait Loci (QTL)) associated with enhanced disease resistance, in particular ASR resistance. In some embodiments the genetic loci or molecular marker associates with the presence of a chromosomal interval comprising the nucleotide sequence or a portion thereof of SEQ ID NOs 1, 2, 3, 4 or 5, wherein the portion thereof associates with ASR resistance.

In some embodiments, methods of producing a disease resistant soybean plant are provided. Such methods may comprise detecting, in a soybean plant or germplasm, the presence of a genetic loci and/or a genetic marker associated with enhanced pathogen resistance (e.g. ASR) and producing a progeny plant from said soybean germplasm.

In some embodiments, methods of selecting a disease resistant soybean plant or germplasm are provided. Such methods may comprise crossing a first soybean plant or germplasm with a second soybean plant or germplasm, wherein the first soybean plant or germplasm comprises a genetic loci derived from any one of plant accessions PI441001, PI441008, PI446958, PI509501, PI583970, PI483224,or a progeny plant thereof comprising any one of SEQ ID NOs 1, 2, 3, 4 or 5 or a portion thereof associated with enhanced disease and/or ASR resistance, and/or tolerance, and selecting a progeny plant or germplasm that possesses the genetic loci.

In some embodiments, methods of introgressing a genetic loci derived from soybean accession numbers PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 associated with enhanced pathogen resistance into a soybean plant or germplasm are provided. Such methods may comprise crossing a first soybean plant or germplasm comprising a chromosomal interval (e.g. SEQ ID Nos: 1, 2, 3, 4 or 5) derived from soybean accession number PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 associated with enhanced pathogen resistance with a second soybean plant or germplasm that lacks said genetic loci and optionally repeatedly backcrossing progeny plants comprising said genetic allele with the second soybean plant or germplasm to produce an soybean plant (e.g. Glycine max) or germplasm with enhanced pathogen resistance comprising the chromosomal interval derived from soybean accession number PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 associated with enhanced ASR resistance. Progeny comprising the chromosomal interval associated with enhanced pathogen resistance may be identified by detecting, in their genomes, the presence of a marker associated with or genetically linked to said chromosomal interval derived from soybean accession number PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval comprises SEQ ID NOs 1, 2, 3, 4 or 5 or a portion thereof and the marker can be any of the favorable alleles as described in Tables 1-5. R-Genes from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 can be introgressed into a Glycine max line through the use of embryo rescue methods known by those skilled in the art for example as is disclosed in U.S. Pat. No. 7,842,850 herein incorporated by reference and through methods as described in the working Examples herein, describing a alternative method of embryo rescue.

Soybean plants and/or germplasms identified, produced or selected by the methods of this invention are also provided, as are any progeny and/or seeds derived from a soybean plant or germplasm identified, produced or selected by these methods. In one embodiment molecular markers associating with the presence of a chromosomal intervals depicted in any one of SEQ ID NOs 1, 2, 3, 4 or 5 may be used to identify or select for plant lines resistant to ASR. Further said molecular markers may be located within 20 cM, 10 cM, ScM, 4 cM, 3 cM, 2 cM, and 1 cM of said chromosomal interval or from any respective favorable allele associated with ASR resistance as depicted in any one of Tables 1-5. In another embodiment, said molecular marker may be located within 20 cM, 10 cM, ScM, 4 cM, 3 cM, 2 cM, 1 cM of any SNP markers associated with ASR as described in any one of Tables 1-5.

Non-naturally occurring soybean seeds, plants and/or germplasms comprising one or genetic loci derived from plant accession number PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 (herein, TI441001′, TI441008′, TI446958′, PI509501″, TI583970′, or TI483224′) associated with enhanced pathogen resistance (e.g. ASR, Cyst Nematode, Phytopthora, etc.) are also provided. In specific embodiments said genetic loci comprise SEQ ID NOs 1, 2, 3, 4 or 5 and/or any favorable alleles as depicted in Tables 1-5.

A marker associated with enhanced pathogen resistance, more specifically ASR, may comprise, consist essentially of or consist of a single allele or a combination of alleles at one or more genetic loci derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 that associate with enhanced pathogen (ASR) resistance. In one embodiment the marker is within a chromosomal interval as described by SEQ ID NOs 1, 2, 3, 4 or 5. In another embodiment the marker is any one of the favorable alleles as depicted in Tables 1-5.

The foregoing and other objects and aspects of the present invention are explained in detail in the drawings and specification set forth below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a depiction of Glycine tomentella SNPs associated with ASR resistance on Glycine tomentella genomic scaffolding located on chromosome 5.

FIG. 2 shows a mapping interval 0.023-1.16Mb on Scaffold 49652 associated with ASR resistance.

FIG. 3 shows a mapping interval 0.02-1.19Mb on Scaffold 46840 associated with ASR resistance.

FIG. 4 is a marker association map for Glycine tomentella (PI441001) where bands indicate regions/intervals of respective chromosomes associated with ASR resistance.

FIG. 5 illustrates the rust rating scale used to measure plant phenotype.

FIG. 6 shows chromosome mapping for ASR resistance QTL for Glycine tomentella PI583970.

FIG. 7 is a marker association map for Glycine tomentella (PI583970) where bands indicate regions/intervals of respective chromosomes associated with ASR resistance.

FIG. 8 shows a mapping interval on scaffold 000819F associated with ASR resistance.

FIG. 9 shows chromosome mapping for ASR resistance QTL for Glycine tomentella PI483224.

FIG. 10 is a marker association map for Glycine tomentella (PI483224) where bands indicate regions/intervals of respective chromosomes associated with ASR resistance.

FIG. 11 shows a mapping interval on scaffold 002687F associated with ASR resistance.

DETAILED DESCRIPTION OF THE INVENTION

The presently disclosed subject matter relates at least in part to the identification of a genomic region (i.e. chromosomal interval(s) on Glycine tomentella Chromosome 5) derived from Glycine tomentella accession lines PI441001, PI441008, PI446958, PI509501, PI583970, PI483224, PI441008 or progeny thereof associated with enhanced ASR resistance. As such, said chromosomal interval from PI441001, PI441008, PI446958, PI509501, PI583970, PI483224, PI441008 or progeny thereof, may be introgressed into Glycine max lines via somatic embryo rescue (see for example U.S. Patent Publication 2007/0261139 and examples herein describing a alternative method of embryo rescue) or through the use of a Glycine max donor line having introgressed into its genome the genetic region from PI441001, PI441008, PI583970, or PI483224, , wherein the region comprises any one of SEQ ID NO: 1-5 or a portion thereof wherein presence of said genetic region is associated with increased or enhanced disease resistance to, for example, ASR, SCN, Stem termination, Stem Canker, Bacterial pustule, root knot nematode, brown stem rot, Frogeye leaf spot, or phytopthora. In another embodiment a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 is introduced into a Glycine max line not comprising said chromosomal interval wherein said introduction confers in the Glycine max line or its progeny increased resistances to disease (e.g. ASR) wherein the said chromosome interval is derived from chromosome 5 of Glycine tomentella and further wherein said chromosomal interval comprises at least one allele that associates with the trait of increased disease resistance, such as ASR, wherein said allele is any one of the alleles respectively selected from any one as depicted in Tables 1-5.

This description is not intended to be a detailed catalog of all the different ways in which the invention may be implemented, or all the features that may be added to the instant invention. For example, features illustrated with respect to one embodiment may be incorporated into other embodiments, and features illustrated with respect to a particular embodiment may be deleted from that embodiment. Thus, the invention contemplates that in some embodiments of the invention, any feature or combination of features set forth herein can be excluded or omitted. In addition, numerous variations and additions to the various embodiments suggested herein will be apparent to those skilled in the art in light of the instant disclosure, which do not depart from the instant invention. Hence, the following descriptions are intended to illustrate some particular embodiments of the invention, and not to exhaustively specify all permutations, combinations and variations thereof.

All references listed below, as well as all references cited in the instant disclosure, including but not limited to all patents, patent applications and publications thereof, scientific journal articles, and database entries (e.g., GENBANK® database entries and all annotations available therein) are incorporated herein by reference in their entireties to the extent that they supplement, explain, provide a background for, or teach methodology, techniques, and/or compositions employed herein.

Definitions

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which the presently disclosed subject matter belongs.

Although the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate understanding of the presently disclosed subject matter.

As used herein, the terms “a” or “an” or “the” may refer to one or more than one. For example, “a” marker can mean one marker or a plurality of markers.

As used herein, the term “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (“or”).

As used herein, the term “about,” when used in reference to a measurable value such as an amount of mass, dose, time, temperature, and the like, is meant to encompass variations of up to 10% of the specified amount.

The term “consists essentially of” (and grammatical variants thereof), as applied to a polynucleotide sequence of this invention, means a polynucleotide sequence that consists of both the recited sequence (e.g., SEQ ID NO) and a total of ten or less (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) additional nucleotides on the 5′ and/or 3′ ends of the recited sequence such that the function of the polynucleotide is not materially altered. The total of ten or less additional nucleotides includes the total number of additional nucleotides on both ends added together. The term “materially altered,” as applied to polynucleotides of the invention, refers to an increase or decrease in ability to express the polynucleotide sequence of at least about 50% or more as compared to the expression level of a polynucleotide sequence consisting of the recited sequence.

The term “introduced” as used herein, in connection to a plant, means accomplished by any manner including but not limited to; introgression, transgenic, Clustered Regularly Interspaced Short Palindromic Repeats modification (CRISPR), Transcription activator-like effector nucleases (TALENs) (Feng et al. 2013, Joung & Sander 2013), meganucleases, or zinc finger nucleases (ZFNs).

As used herein, the term “wild glycine” refers to a perennial Glycine plant, for example any one of G. canescens, G. argyrea, G. clandestine, G. latrobeana, G. albicans, G. aphyonota, G. arenaria, G. curvata, G. cyrtoloba, G. dolichocarpa, G. falcate, G. gracei, G. hirticaulis, G. lactovirens, G. latifolia, G. microphylla, G. montis-douglas, G. peratosa, G. pescadrensis, G. pindanica, G. pullenii, G. rubiginosa, G. stenophita, G. syndetika, orG. tomentella.

As used herein, the term “allele” refers to one of two or more different nucleotides or nucleotide sequences that occur at a specific locus.

A marker is “associated with” a trait when it is linked to it and when the presence of the marker is an indicator of whether and/or to what extent the desired trait or trait form will occur in a plant/germplasm comprising the marker. Similarly, a marker is “associated with” an allele when it is linked to it and when the presence of the marker is an indicator of whether the allele is present in a plant/germplasm comprising the marker. For example, “a marker associated with enhanced pathogen resistance” refers to a marker whose presence or absence can be used to predict whether and/or to what extent a plant will display a pathogen resistant phenotype (e.g. any favorable SNP allele as described in Tables 1-5 are “associated with” ASR resistance in a soybean plant).

As used herein, the terms “backcross” and “backcrossing” refer to the process whereby a progeny plant is repeatedly crossed back to one of its parents. In a backcros sing scheme, the “donor” parent refers to the parental plant with the desired gene or locus to be introgressed. The “recipient” parent (used one or more times) or “recurrent” parent (used two or more times) refers to the parental plant into which the gene or locus is being introgressed. For example, see Ragot, M. et al. Marker-assisted Backcrossing: A Practical Example, in TECHNIQUES ET UTILISATIONS DES MARQUEURS MOLECULAIRES LES COLLOQUES, Vol. 72, pp. 45-56 (1995); and Openshaw et al., Marker-assisted Selection in Backcross Breeding, in PROCEEDINGS OF THE SYMPOSIUM “ANALYSIS OF MOLECULAR MARKER DATA,” pp. 41-53 (1994). The initial cross gives rise to the F1 generation. The term “BC1” refers to the second use of the recurrent parent, “BC2” refers to the third use of the recurrent parent, and so on.

A centimorgan (“cM”) is a unit of measure of recombination frequency. One cM is equal to a 1% chance that a marker at one genetic locus will be separated from a marker at a second locus due to crossing over in a single generation.

As used herein, the term “chromosomal interval defined by and including,” used in reference to particular loci and/or alleles, refers to a chromosomal interval delimited by and encompassing the stated loci/alleles.

As used herein, the terms “cross” or “crossed” refer to the fusion of gametes via pollination to produce progeny (e.g., cells, seeds or plants). The term encompasses both sexual crosses (the pollination of one plant by another) and selfing (self-pollination, e.g., when the pollen and ovule are from the same plant). The term “crossing” refers to the act of fusing gametes via pollination to produce progeny.

As used herein, the terms “cultivar” and “variety” refer to a group of similar plants that by structural or genetic features and/or performance can be distinguished from other varieties within the same species.

As used herein, the terms “desired allele”, “favorable allele” and “allele of interest” are used interchangeably to refer to an allele associated with a desired trait (e.g. ASR resistance).

As used herein, the terms “enhanced pathogen resistance” or “enhanced disease resistance” refers to an improvement, enhancement, or increase in a plant's ability to endure and/or thrive despite being infected with a disease (e.g. Asian soybean rust) as compared to one or more control plants (e.g., one or both of the parents, or a plant lacking a marker associated with enhanced pathogen resistance to respective pathogen/disease). Enhanced disease resistance includes any mechanism (other than whole-plant immunity or resistance) that reduces the expression of symptoms indicative of infection for a respective disease such as Asian soybean rust, soybean cyst nematode, Pytophthora, etc.

An “elite line” or “elite strain” is an agronomically superior line that has resulted from many cycles of breeding and selection for superior agronomic performance. Numerous elite lines are available and known to those of skill in the art of soybean breeding. An “elite population” is an assortment of elite individuals or lines that can be used to represent the state of the art in terms of agronomically superior genotypes of a given crop species, such as soybean. Similarly, an “elite germplasm” or elite strain of germplasm is an agronomically superior germplasm, typically derived from and/or capable of giving rise to a plant with superior agronomic performance, such as an existing or newly developed elite line of soybean.

An “elite” plant is any plant from an elite line, such that an elite plant is a representative plant from an elite variety. Non-limiting examples of elite soybean varieties that are commercially available to farmers or soybean breeders include: AG00802, A0868, AG0902, A1923, AG2403, A2824, A3704, A4324, A5404, AG5903, AG6202 AG0934; AG1435; AG2031; AG2035; AG2433; AG2733; AG2933; AG3334; AG3832; AG4135; AG4632; AG4934; AG5831; AG6534; and AG7231 (Asgrow Seeds, Des Moines, Iowa, USA); BPRO144RR, BPR 4077NRR and BPR 4390NRR (Bio Plant Research, Camp Point, Ill., USA); DKB17-51 and DKB37-51 (DeKalb Genetics, DeKalb, Ill., USA); DP 4546 RR, and DP 7870 RR (Delta & Pine Land Company, Lubbock, Tex., USA); JG 03R501, JG 32R606C ADD and JG 55R503C (JGL Inc., Greencastle, Ind., USA); NKS 13-K2 (NK Division of Syngenta Seeds, Golden Valley, Minn., USA); 90M01, 91M30, 92M33, 93M11, 94M30, 95M30, 97B52, P008T22R2; P16T17R2; P22T69R; P25T51R; P34T07R2; P35T58R; P39T67R; P47T36R; P46T21R; and P56T03R2 (Pioneer Hi-Bred International, Johnston, Iowa, USA); SG4771NRR and SG5161NRR/STS (Soygenetics, LLC, Lafayette, Ind., USA); S00-K5, S11-L2, S28-Y2, S43-B1, S53-Al, S76-L9, S78-G6, 50009-M2; 5007-Y4; 504-D3; S14-A6; S20-T6; S21-M7; S26-P3; S28-N6; S30-V6; S35-C3; S36-Y6; S39-C4; S47-K5; S48-D9; S52-Y2; S58-Z4; S67-R6; S73-S8; and S78-G6 (Syngenta Seeds, Henderson, Ky., USA); Richer (Northstar Seed Ltd. Alberta, Calif.); 14RD62 (Stine Seed Co. Iowa., USA); or Armor 4744 (Armor Seed, LLC, Ark., USA).

The terms “agronomically elite” as used herein, means a genotype that has a culmination of many distinguishable traits such as emergence, vigor, vegetative vigor, disease resistance, seed set, standability, yield and threshability which allows a producer to harvest a product of commercial significance.

As used herein, the term “commercially significant yield” or “agronomically acceptable yield” refers to a grain yield of at least 100% of a commercial check variety such as AG2703 or DKB23-51.

As used herein, the terms “exotic,” “exotic line” and “exotic germplasm” refer to any plant, line or germplasm that is not elite. In general, exotic plants/germplasms are not derived from any known elite plant or germplasm, but rather are selected to introduce one or more desired genetic elements into a breeding program (e.g., to introduce novel alleles into a breeding program).

A “genetic map” is a description of genetic linkage relationships among loci on one or more chromosomes within a given species, generally depicted in a diagrammatic or tabular form. For each genetic map, distances between loci are measured by the recombination frequencies between them. Recombinations between loci can be detected using a variety of markers. A genetic map is a product of the mapping population, types of markers used, and the polymorphic potential of each marker between different populations. The order and genetic distances between loci can differ from one genetic map to another.

As used herein, the term “genotype” refers to the genetic constitution of an individual (or group of individuals) at one or more genetic loci, as contrasted with the observable and/or detectable and/or manifested trait (the phenotype). Genotype is defined by the allele(s) of one or more known loci that the individual has inherited from its parents. The term genotype can be used to refer to an individual's genetic constitution at a single locus, at multiple loci, or more generally, the term genotype can be used to refer to an individual's genetic make-up for all the genes in its genome. Genotypes can be indirectly characterized, e.g., using markers and/or directly characterized by nucleic acid sequencing.

As used herein, the term “germplasm” refers to genetic material of or from an individual (e.g., a plant), a group of individuals (e.g., a plant line, variety or family), or a clone derived from a line, variety, species, or culture. The germplasm can be part of an organism or cell, or can be separate from the organism or cell. In general, germplasm provides genetic material with a specific molecular makeup that provides a physical foundation for some or all of the hereditary qualities of an organism or cell culture. As used herein, germplasm may refer to seeds, cells (including protoplasts and calli) or tissues from which new plants may be grown, as well as plant parts that can be cultured into a whole plant (e.g., stems, buds, roots, leaves, etc.).

A “haplotype” is the genotype of an individual at a plurality of genetic loci, i.e., a combination of alleles. Typically, the genetic loci that define a haplotype are physically and genetically linked, i.e., on the same chromosome segment. The term “haplotype” can refer to polymorphisms at a particular locus, such as a single marker locus, or polymorphisms at multiple loci along a chromosomal segment.

As used herein, the term “heterozygous” refers to a genetic status wherein different alleles reside at corresponding loci on homologous chromosomes.

As used herein, the term “homozygous” refers to a genetic status wherein identical alleles reside at corresponding loci on homologous chromosomes.

As used herein, the term “hybrid” refers to a seed and/or plant produced when at least two genetically dissimilar parents are crossed.

As used herein, the term “inbred” refers to a substantially homozygous plant or variety. The term may refer to a plant or variety that is substantially homozygous throughout the entire genome or that is substantially homozygous with respect to a portion of the genome that is of particular interest.

As used herein, the term “indel” refers to an insertion or deletion in a pair of nucleotide sequences, wherein a first sequence may be referred to as having an insertion relative to a second sequence or the second sequence may be referred to as having a deletion relative to the first sequence.

As used herein, the terms “introgression,” “introgressing” and “introgressed” refer to both the natural and artificial transmission of a desired allele or combination of desired alleles of a genetic locus or genetic loci from one genetic background to another. For example, a desired allele at a specified locus can be transmitted to at least one progeny via a sexual cross between two parents of the same species, where at least one of the parents has the desired allele in its genome. Alternatively, for example, transmission of an allele can occur by recombination between two donor genomes, e.g., in a fused protoplast, where at least one of the donor protoplasts has the desired allele in its genome. The desired allele may be a selected allele of a marker, a QTL, a transgene, or the like. Offspring comprising the desired allele can be repeatedly backcrossed to a line having a desired genetic background and selected for the desired allele, with the result being that the desired allele becomes fixed in the desired genetic background. For example, a marker associated with enhanced ASR tolerance may be introgressed from a donor into a recurrent parent that is not disease resistant. The resulting offspring could then be repeatedly backcrossed and selected until the progeny possess the ASR tolerance allele(s) in the recurrent parent background.

As used herein, the term “linkage” refers to the degree with which one marker locus is associated with another marker locus or some other locus (for example, an ASR tolerance locus). The linkage relationship between a molecular marker and a phenotype may be given as a “probability” or “adjusted probability.” Linkage can be expressed as a desired limit or range. For example, in some embodiments, any marker is linked (genetically and physically) to any other marker when the markers are separated by less than about 50, 40, 30, 25, 20, or 15 map units (or cM). For example, embodiments of the invention herein, provide for marker loci closely linked to ASR resistant chromosomal intervals comprising a nucleotide sequence of any one of SEQ ID NOs 1-5.

In some aspects of the present invention, it is advantageous to define a bracketed range of linkage, for example, from about 10 cM and about 20 cM, from about 10 cM and about 30 cM, or from about 10 cM and about 40 cM. The more closely a marker is linked to a second locus, the better an indicator for the second locus that marker becomes. Thus, “closely linked loci” such as a marker locus and a second locus display an inter-locus recombination frequency of about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, or 2% or less. In some embodiments, the relevant loci display a recombination frequency of about 1% or less, e.g., about 0.75%, 0.5%, 0.25% or less. Two loci that are localized to the same chromosome, and at such a distance that recombination between the two loci occurs at a frequency of less than about 10% (e.g., about 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, or 0.25%, or less) may also be said to be “proximal to” each other. Since one cM is the distance between two markers that show a 1% recombination frequency, any marker is closely linked (genetically and physically) to any other marker that is in close proximity, e.g., at or less than about 10 cM distant. Two closely linked markers on the same chromosome may be positioned about 9, 8, 7, 6, 5, 4, 3, 2, 1, 0.75, 0.5 or 0.25 cM or less from each other.

As used herein, the term “linkage disequilibrium” refers to a non-random segregation of genetic loci or traits (or both). In either case, linkage disequilibrium implies that the relevant loci are within sufficient physical proximity along a length of a chromosome so that they segregate together with greater than random (i.e., non-random) frequency (in the case of co-segregating traits, the loci that underlie the traits are in sufficient proximity to each other). Markers that show linkage disequilibrium are considered linked. Linked loci co-segregate more than 50% of the time, e.g., from about 51% to about 100% of the time. In other words, two markers that co-segregate have a recombination frequency of less than 50% (and, by definition, are separated by less than 50 cM on the same chromosome). As used herein, linkage can be between two markers, or alternatively between a marker and a phenotype. A marker locus can be “associated with” (linked to) a trait, e.g., Asian Soybean Rust. The degree of linkage of a molecular marker to a phenotypic trait is measured, e.g., as a statistical probability of co-segregation of that molecular marker with the phenotype.

Linkage disequilibrium is most commonly assessed using the measure r², which is calculated using the formula described by Hill and Robertson, Theor. Appl. Genet. 38:226 (1968). When r²=1, complete linkage disequilibrium exists between the two marker loci, meaning that the markers have not been separated by recombination and have the same allele frequency. Values for r² above 1/3 indicate sufficiently strong linkage disequilibrium to be useful for mapping. Ardlie et al., Nature Reviews Genetics 3:299 (2002). Hence, alleles are in linkage disequilibrium when r² values between pairwise marker loci are greater than or equal to about 0.33, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or 1.0.

As used herein, the term “linkage equilibrium” describes a situation where two markers independently segregate, i.e., sort among progeny randomly. Markers that show linkage equilibrium are considered unlinked (whether or not they lie on the same chromosome).

A “locus” is a position on a chromosome where a gene or marker or allele is located. In some embodiments, a locus may encompass one or more nucleotides.

As used herein, the terms “marker” and “genetic marker” are used interchangeably to refer to a nucleotide and/or a nucleotide sequence that has been associated with a phenotype, trait or trait form. In some embodiments, a marker may be associated with an allele or alleles of interest and may be indicative of the presence or absence of the allele or alleles of interest in a cell or organism. A marker may be, but is not limited to, an allele, a gene, a haplotype, a restriction fragment length polymorphism (RFLP), a simple sequence repeat (SSR), random amplified polymorphic DNA (RAPD), cleaved amplified polymorphic sequences (CAPS) (Rafalski and Tingey, Trends in Genetics 9:275 (1993)), an amplified fragment length polymorphism (AFLP) (Vos et al., Nucleic Acids Res. 23:4407 (1995)), a single nucleotide polymorphism (SNP) (Brookes, Gene 234:177 (1993)), a sequence-characterized amplified region (SCAR) (Paran and Michelmore, Theor. Appl. Genet. 85:985 (1993)), a sequence-tagged site (STS) (Onozaki et al., Euphytica 138:255 (2004)), a single-stranded conformation polymorphism (SSCP) (Orita et al., Proc. Natl. Acad. Sci. USA 86:2766 (1989)), an inter-simple sequence repeat (ISSR) (Blair et al., Theor. Appl. Genet. 98:780 (1999)), an inter-retrotransposon amplified polymorphism (IRAP), a retrotransposon-microsatellite amplified polymorphism (REMAP) (Kalendar et al., Theor. Appl. Genet. 98:704 (1999)), a chromosome interval, or an RNA cleavage product (such as a Lynx tag). A marker may be present in genomic or expressed nucleic acids (e.g., ESTs). The term marker may also refer to nucleic acids used as probes or primers (e.g., primer pairs) for use in amplifying, hybridizing to and/or detecting nucleic acid molecules according to methods well known in the art. A large number of soybean molecular markers are known in the art, and are published or available from various sources, such as the SoyBase internet resource.

Markers corresponding to genetic polymorphisms between members of a population can be detected by methods well-established in the art. These include, e.g., nucleic acid sequencing, hybridization methods, amplification methods (e.g., PCR-based sequence specific amplification methods), detection of restriction fragment length polymorphisms (RFLP), detection of isozyme markers, detection of polynucleotide polymorphisms by allele specific hybridization (ASH), detection of amplified variable sequences of the plant genome, detection of self-sustained sequence replication, detection of simple sequence repeats (SSRs), detection of single nucleotide polymorphisms (SNPs), and/or detection of amplified fragment length polymorphisms (AFLPs). Well established methods are also known for the detection of expressed sequence tags (ESTs) and SSR markers derived from EST sequences and randomly amplified polymorphic DNA (RAPD).

A “marker allele,” also described as an “allele of a marker locus,” can refer to one of a plurality of polymorphic nucleotide sequences found at a marker locus in a population that is polymorphic for the marker locus.

“Marker-assisted selection” (MAS) is a process by which phenotypes are selected based on marker genotypes. In some embodiments, marker genotypes are used to identify plants that will be selected for a breeding program or for planting. In some embodiments, marker genotypes are used to identify plants that will not be selected for a breeding program or for planting (i.e., counter-selected plants), allowing them to be removed from the breeding/planting population.

As used herein, the terms “marker locus” and “marker loci” refer to a specific chromosome location or locations in the genome of an organism where a specific marker or markers can be found. A marker locus can be used to track the presence of a second linked locus, e.g., a linked locus that encodes or contributes to expression of a phenotypic trait. For example, a marker locus can be used to monitor segregation of alleles at a locus, such as a QTL or single gene, that are genetically or physically linked to the marker locus.

As used herein, the terms “marker probe” and “probe” refer to a nucleotide sequence or nucleic acid molecule that can be used to detect the presence of one or more particular alleles within a marker locus (e.g., a nucleic acid probe that is complementary to all of or a portion of the marker or marker locus, through nucleic acid hybridization). Marker probes comprising about 8, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more contiguous nucleotides may be used for nucleic acid hybridization. Alternatively, in some aspects, a marker probe refers to a probe of any type that is able to distinguish (i.e., genotype) the particular allele that is present at a marker locus.

As used herein, the terms “molecular marker” or “genetic marker” may be used to refer to a genetic marker, as defined above, or an encoded product thereof (e.g., a protein) used as a point of reference when identifying a linked locus. A molecular marker can be derived from genomic nucleotide sequences or from expressed nucleotide sequences (e.g., from a spliced RNA, a cDNA, etc.). The term also refers to nucleotide sequences complementary to or flanking the marker sequences, such as nucleotide sequences used as probes and/or primers capable of amplifying the marker sequence. Nucleotide sequences are “complementary” when they specifically hybridize in solution, e.g., according to Watson-Crick base pairing rules. Some of the markers described herein are also referred to as hybridization markers when located on an indel region. This is because the insertion region is, by definition, a polymorphism vis-ã-vis a plant without the insertion. Thus, the marker need only indicate whether the indel region is present or absent. Any suitable marker detection technology may be used to identify such a hybridization marker, e.g., SNP technology is used in the examples provided herein.

A “non-naturally occurring variety of soybean” is any variety of soybean that does not naturally exist in nature. A “non-naturally occurring variety of soybean” may be produced by any method known in the art, including, but not limited to, transforming a soybean plant or germplasm, transfecting a soybean plant or germplasm and crossing a naturally occurring variety of soybean with a non-naturally occurring variety of soybean. In some embodiments, a “non-naturally occurring variety of soybean” may comprise one of more heterologous nucleotide sequences. In some embodiments, a “non-naturally occurring variety of soybean” may comprise one or more non-naturally occurring copies of a naturally occurring nucleotide sequence (i.e., extraneous copies of a gene that naturally occurs in soybean). In some embodiments, a “non-naturally occurring variety of soybean” may comprise a non-natural combination of two or more naturally occurring nucleotide sequences (i.e., two or more naturally occurring genes that do not naturally occur in the same soybean, for instance genes not found in Glycine max lines).

As used herein, the term “primer” refers to an oligonucleotide which is capable of annealing to a nucleic acid target and serving as a point of initiation of DNA synthesis when placed under conditions in which synthesis of a primer extension product is induced (e.g., in the presence of nucleotides and an agent for polymerization such as DNA polymerase and at a suitable temperature and pH). A primer (in some embodiments an extension primer and in some embodiments an amplification primer) is in some embodiments single stranded for maximum efficiency in extension and/or amplification. In some embodiments, the primer is an oligodeoxyribonucleotide. A primer is typically sufficiently long to prime the synthesis of extension and/or amplification products in the presence of the agent for polymerization. The minimum length of the primer can depend on many factors, including, but not limited to temperature and composition (A/T vs. G/C content) of the primer. In the context of amplification primers, these are typically provided as a pair of bi-directional primers consisting of one forward and one reverse primer or provided as a pair of forward primers as commonly used in the art of DNA amplification such as in PCR amplification. As such, it will be understood that the term “primer,” as used herein, can refer to more than one primer, particularly in the case where there is some ambiguity in the information regarding the terminal sequence(s) of the target region to be amplified. Hence, a “primer” can include a collection of primer oligonucleotides containing sequences representing the possible variations in the sequence or includes nucleotides which allow a typical base pairing. Primers can be prepared by any suitable method known in the art. Methods for preparing oligonucleotides of specific sequence are known in the art, and include, for example, cloning and restriction of appropriate sequences and direct chemical synthesis. Chemical synthesis methods can include, for example, the phospho di- or tri-ester method, the diethylphosphoramidate method and the solid support method disclosed in U.S. Pat. No. 4,458,066. Primers can be labeled, if desired, by incorporating detectable moieties by for instance spectroscopic, fluorescence, photochemical, biochemical, immunochemical, or chemical moieties. Primers diagnostic (i.e. able to identify or select based on presence of ASR resistant alleles) for ASR resistance can be created to any favorable SNP as described in any one of Tables 1-5. The PCR method is well described in handbooks and known to the skilled person. After amplification by PCR, target polynucleotides can be detected by hybridization with a probe polynucleotide, which forms a stable hybrid with the target sequence under stringent to moderately stringent hybridization and wash conditions. If it is expected that the probes are essentially completely complementary (i.e., about 99% or greater) to the target sequence, stringent conditions can be used. If some mismatching is expected, for example if variant strains are expected with the result that the probe will not be completely complementary, the stringency of hybridization can be reduced. In some embodiments, conditions are chosen to rule out non-specific/adventitious binding. Conditions that affect hybridization, and that select against non-specific binding are known in the art, and are described in, for example, Sambrook & Russell (2001). Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., United States of America. Generally, lower salt concentration and higher temperature hybridization and/or washes increase the stringency of hybridization conditions.

As used herein, the terms “phenotype,” “phenotypic trait” or “trait” refer to one or more traits and/or manifestations of an organism. The phenotype can be a manifestation that is observable to the naked eye, or by any other means of evaluation known in the art, e.g., microscopy, biochemical analysis, or an electromechanical assay. In some cases, a phenotype or trait is directly controlled by a single gene or genetic locus, i.e., a “single gene trait.” In other cases, a phenotype or trait is the result of several genes. It is noted that, as used herein, the term “disease resistant phenotype” takes into account environmental conditions that might affect the respective disease such that the effect is real and reproducible.

As used herein, the term “plant” may refer to a whole plant, any part thereof, or a cell or tissue culture derived from a plant. Thus, the term “plant” can refer to any of: whole plants, plant components or organs (e.g., roots, stems, leaves, buds, flowers, pods, etc.), plant tissues, seeds and/or plant cells. A plant cell is a cell of a plant, taken from a plant, or derived through culture from a cell taken from a plant. Thus, the term “soybean plant” may refer to a whole soybean plant, one or more parts of a soybean plant (e.g., roots, root tips, stems, leaves, buds, flowers, pods, seeds, cotyledons, etc.), soybean plant cells, soybean plant protoplasts and/or soybean plant calli.

As used herein, the term “plant part” includes but is not limited to embryos, pollen, seeds, leaves, flowers (including but not limited to anthers, ovules and the like), fruit, stems or branches, roots, root tips, cells including cells that are intact in plants and/or parts of plants, protoplasts, plant cell tissue cultures, plant calli, plant clumps, and the like. Thus, a plant part includes soybean tissue culture from which soybean plants can be regenerated. Further, as used herein, “plant cell” refers to a structural and physiological unit of the plant, which comprises a cell wall and also may refer to a protoplast. A plant cell of the present invention can be in the form of an isolated single cell or can be a cultured cell or can be a part of a higher-organized unit such as, for example, a plant tissue or a plant organ.

As used herein, the term “polymorphism” refers to a variation in the nucleotide sequence at a locus, where said variation is too common to be due merely to a spontaneous mutation. A polymorphism can be a single nucleotide polymorphism (SNP) or an insertion/deletion polymorphism, also referred to herein as an “indel.” Additionally, the variation can be in a transcriptional profile or a methylation pattern. The polymorphic site or sites of a nucleotide sequence can be determined by comparing the nucleotide sequences at one or more loci in two or more germplasm entries.

As used herein, the terms “closely linked” refers to linked markers displaying a cross over frequency with a given marker of about 10% or less (e.g. the given marker is within about 10 cM of a closely linked ASR marker). Put another way, closely linked loci co-segregate at least about 90% of the time. With regard to physical position on a chromosome, closely linked markers can be separated, for example, by about 1 megabase (Mb; 1 million nucleotides), about 500 kilobases (Kb; 1000 nucleotides), about 400 Kb, about 300 Kb, about 200 Kb, about 100 Kb, about 50 Kb, about 25 Kb, about 10 Kb, about 5 Kb, about 4 Kb, about 3 Kb, about 2 Kb, about 1 Kb, about 500 nucleotides, about 250 nucleotides, or less.

As used herein, the term “population” refers to a genetically heterogeneous collection of plants sharing a common genetic derivation.

As used herein, the terms “progeny” and “progeny plant” refer to a plant generated from a vegetative or sexual reproduction from one or more parent plants. A progeny plant may be obtained by cloning or selfing a single parent plant, or by crossing two parental plants.

As used herein, the term “reference sequence” refers to a defined nucleotide sequence used as a basis for nucleotide sequence comparison. The reference sequence for a marker, for example, is obtained by genotyping a number of lines at the locus or loci of interest, aligning the nucleotide sequences in a sequence alignment program, and then obtaining the consensus sequence of the alignment. Hence, a reference sequence identifies the polymorphisms in alleles at a locus. A reference sequence may not be a copy of an actual nucleic acid sequence from any particular organism; however, it is useful for designing primers and probes for actual polymorphisms in the locus or loci.

As used herein, the terms “disease tolerance” and “disease resistant” refer to a plant's ability to endure and/or thrive despite being infected with a respective disease. When used in reference to germplasm, the terms refer to the ability of a plant that arises from that germplasm to endure and/or thrive despite being infected with a respective disease. In some embodiments, infected Disease resistant soybean plants may yield as well (or nearly as well) as uninfected soybean plants. In general, a plant or germplasm is labeled as “Disease resistant” if it displays “enhanced pathogen resistance.”

An “unfavorable allele” of a marker is a marker allele that segregates with the unfavorable plant phenotype, therefore providing the benefit of identifying plants that can be removed from a breeding program or planting. For instance, one could eliminate from a plant breeding program plant lines carrying unfavorable alleles for ASR resistance.

“PI441001, PI441008, PI583970, or PI483224,” refers to Glycine tomentella plant accession number PI441001, PI441008, PI583970, or PI483224.

Genetic Mapping

Genetic loci correlating with particular phenotypes, such as disease resistance, can be mapped in an organism's genome. By identifying a marker or cluster of markers that co-segregate with a trait of interest, the breeder is able to rapidly select a desired phenotype by selecting for the proper marker (a process called marker-assisted selection, or “MAS”). Such markers may also be used by breeders to design genotypes in silico and to practice whole genome selection.

The present invention provides markers associated with enhanced disease resistance. Detection of these markers and/or other linked markers can be used to identify, select and/or produce disease resistant, more specifically ASR resistant, plants and/or to eliminate plants that are not disease resistant from breeding programs or planting.

Glycine Tomentella Genetic Loci Associated with Enhanced Disease Resistance

Markers associated with enhanced disease resistance are identified herein (see Tables 1-5 indicating favorable markers associated with enhanced ASR resistance). A marker of the present invention may comprise a single allele or a combination of alleles at one or more genetic loci (for example, any combination of a favorable markers from Tables 1- 5). For example, the marker may comprise one or more marker alleles located within a first chromosomal interval (e.g. SEQ ID NO: 1) and one or more marker alleles located within a second chromosomal interval (e.g. SEQ ID NO: 2).

Marker-Assisted Selection

Markers can be used in a variety of plant breeding applications. See, e.g., Staub et al., Hortscience 31: 729 (1996); Tanksley, Plant Molecular Biology Reporter 1: 3 (1983). One of the main areas of interest is to increase the efficiency of backcros sing and introgressing genes using marker-assisted selection (MAS). In general, MAS takes advantage of genetic markers that have been identified as having a significant likelihood of co-segregation with a desired trait. Such markers are presumed to be in/near the gene(s) that give rise to the desired phenotype, and their presence indicates that the plant will possess the desired trait. Plants which possess the marker are expected to transfer the desired phenotype to their progeny.

A marker that demonstrates linkage with a locus affecting a desired phenotypic trait provides a useful tool for the selection of the trait in a plant population. This is particularly true where the phenotype is hard to assay or occurs at a late stage in plant development. Since DNA marker assays are less laborious and take up less physical space than field phenotyping, much larger populations can be assayed, increasing the chances of finding a recombinant with the target segment from the donor line moved to the recipient line. The closer the linkage, the more useful the marker, as recombination is less likely to occur between the marker and the gene causing or imparting the trait. Having flanking markers decreases the chances that false positive selection will occur. The ideal situation is to have a marker within the causative gene itself, so that recombination cannot occur between the marker and the gene. Such a marker is called a “perfect marker”.

When a gene is introgressed by MAS, it is not only the gene that is introduced but also the flanking regions. Gepts, Crop Sci 42:1780 (2002). This is referred to as “linkage drag.” In the case where the donor plant is highly unrelated to the recipient plant, these flanking regions carry additional genes that may code for agronomically undesirable traits. This “linkage drag” may also result in reduced yield or other negative agronomic characteristics even after multiple cycles of backcrossing into the elite soybean line. This is also sometimes referred to as “yield drag.” The size of the flanking region can be decreased by additional backcrossing, although this is not always successful, as breeders do not have control over the size of the region or the recombination breakpoints. Young et al., Genetics 120:579 (1998). In classical breeding, it is usually only by chance that recombinations that contribute to a reduction in the size of the donor segment are selected. Tanksley et al., Biotechnology 7: 257 (1989). Even after 20 backcrosses, one might find a sizeable piece of the donor chromosome still linked to the gene being selected. With markers, however, it is possible to select those rare individuals that have experienced recombination near the gene of interest. In 150 backcross plants, there is a 95% chance that at least one plant will have experienced a crossover within 1 cM of the gene, based on a single meiosis map distance. Markers allow for unequivocal identification of those individuals. With one additional backcross of 300 plants, there would be a 95% chance of a crossover within 1 cM single meiosis map distance of the other side of the gene, generating a segment around the target gene of less than 2 cM based on a single meiosis map distance. This can be accomplished in two generations with markers, while it would have required on average 100 generations without markers. See Tanksley et al., supra. When the exact location of a gene is known, flanking markers surrounding the gene can be utilized to select for recombinations in different population sizes. For example, in smaller population sizes, recombinations may be expected further away from the gene, so more distal flanking markers would be required to detect the recombination.

The availability of integrated linkage maps of the soybean genome containing increasing densities of public soybean markers has facilitated soybean genetic mapping and MAS.

Of all the molecular marker types, SNPs are the most abundant and have the potential to provide the highest genetic map resolution. Bhattramakki et al., Plant Molec. Biol. 48:539 (2002). SNPs can be assayed in a so-called “ultra-high-throughput” fashion because they do not require large amounts of nucleic acid and automation of the assay is straight-forward. SNPs also have the benefit of being relatively low-cost systems. These three factors together make SNPs highly attractive for use in MAS. Several methods are available for SNP genotyping, including but not limited to, hybridization, primer extension, oligonucleotide ligation, nuclease cleavage, minisequencing and coded spheres. Such methods have been reviewed in various publications: Gut, Hum. Mutat. 17:475 (2001); Shi, Clin. Chem. 47:164 (2001); Kwok, Pharmacogenomics 1:95 (2000); Bhattramakki and Rafalski, Discovery and Application of Single Nucleotide Polymorphism Markers in Plants, in PLANT GENOTYPING: THE DNA FINGERPRINTING OF PLANTS, CABI Publishing, Wallingford (2001). A wide range of commercially available technologies utilize these and other methods to interrogate SNPs, including Masscode™ (Qiagen, Germantown, Md.), Invader® (Hologic, Madison, Wis.), SnapShot® (Applied Biosystems, Foster City, Calif.), Taqman® (Applied Biosystems, Foster City, Calif.) and Beadarrays™ (Illumina, San Diego, Calif.).

A number of SNP alleles together within a sequence, or across linked sequences, can be used to describe a haplotype for any particular genotype. Ching et al., BMC Genet. 3:19 (2002); Gupta et al., (2001), Rafalski, Plant Sci. 162:329 (2002b). Haplotypes can be more informative than single SNPs and can be more descriptive of any particular genotype. For example, a single SNP may be allele “T” for a specific Disease resistant line or variety, but the allele “T” might also occur in the soybean breeding population being utilized for recurrent parents. In this case, a combination of alleles at linked SNPs may be more informative. Once a unique haplotype has been assigned to a donor chromosomal region, that haplotype can be used in that population or any subset thereof to determine whether an individual has a particular gene. The use of automated high throughput marker detection platforms known to those of ordinary skill in the art makes this process highly efficient and effective.

The markers of the present invention can be used in marker-assisted selection protocols to identify and/or select progeny with enhanced Asian soybean rust resistance. Such methods can comprise, consist essentially of or consist of crossing a first soybean plant or germplasm with a second soybean plant or germplasm, wherein the first soybean plant or germplasm comprises a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1 or wherein the chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2, and selecting a progeny plant that possesses the marker. Either of the first and second soybean plants, or both, may be of a non-naturally occurring variety of soybean. In some embodiments, the second soybean plant or germplasm is of an elite variety of soybean. In some embodiments, the genome of the second soybean plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean. In another embodiment, the first soybean plant comprises the chromosomal interval a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1 or wherein the chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2 wherein the chromosome interval further comprises at least one allele as depicted in any of Tables 1-5

Methods for identifying and/or selecting a disease resistant soybean plant or germplasm may comprise, consist essentially of or consist of detecting the presence of a marker associated with enhanced ASR tolerance. The marker may be detected in any sample taken from the plant or germplasm, including, but not limited to, the whole plant or germplasm, a portion of said plant or germplasm (e.g., a seed chip, a leaf punch disk or a cell from said plant or germplasm) or a nucleotide sequence from said plant or germplasm. Such a sample may be taken from the plant or germplasm using any present or future method known in the art, including, but not limited to, automated methods of removing a portion of endosperm with a sharp blade, drilling a small hole in the seed and collecting the resultant powder, cutting the seed with a laser and punching a leaf disk. The soybean plant may be of a non-naturally occurring variety of soybean. In some embodiments, the genome of the soybean plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean.

In some embodiments, the marker detected in the sample may comprise, consist essentially of or consist of one or more marker alleles located within a chromosomal interval selected from the group consisting of:

-   -   1) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 1251375 of SEQ ID NO: 1; or     -   2) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 2515428 of SEQ ID NO: 2.; or     -   3) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 365842 of SEQ ID NO: 3.; or     -   4) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 646429 of SEQ ID NO: 4.;     -   5) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 750080 of SEQ ID NO: 5; or     -   6) A chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1         cM, 0.5 cM from a SNP marker that associates with increased ASR         resistance in soybean wherein the SNP marker is selected from         the group consisting of any favorable SNP marker displayed in         Tables 1-5.

Methods for producing an disease resistant soybean plant may comprise, consist essentially of or consist of detecting, in a germplasm, a marker associated with enhanced disease resistance (e.g. ASR) wherein said marker is selected from Tables 1-5 or wherein marker is a closely linked loci of any marker described in any one of Tables 1-5 and producing a soybean plant from said germplasm. The marker may be detected in any sample taken from the germplasm, including, but not limited to, a portion of said germplasm (e.g., a seed chip or a cell from said germplasm) or a nucleotide sequence from said germplasm. Such a sample may be taken from the germplasm using any present or future method known in the art, including, but not limited to, automated methods of removing a portion of endosperm with a sharp blade, drilling a small hole in the seed and collecting the resultant powder, cutting the seed with a laser and punching a leaf disk. The germplasm may be of a non-naturally occurring variety of soybean. In some embodiments, the genome of the germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean. A disease resistant soybean plant is then produced from the germplasm identified as having the marker associated with enhanced disease resistance (e.g. ASR) according to methods well known in the art for breeding and producing plants from germplasm.

In some embodiments, the marker detected in the germplasm may comprise, consist essentially of or consist of one or more marker alleles located within a chromosomal interval selected from the group consisting of:

1) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or

-   -   2) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 2515428 of SEQ ID NO: 2.; or     -   3) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 365842 of SEQ ID NO: 3.; or     -   4) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 646429 of SEQ ID NO: 4.;     -   5) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 750080 of SEQ ID NO: 5;or     -   6) A chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1         cM, 0.5 cM from a SNP marker that associates with increased ASR         resistance in soybean wherein the SNP marker is selected from         the group consisting of any favorable SNP marker displayed in         Tables 1-5.

In some embodiments, the marker detected in the germplasm may comprise, consist essentially of or consist of one or more marker alleles selected from any of Tables 1-5.

Methods for producing and/or selecting an Asian soy rust resistant/tolerant soybean plant or germplasm may comprise crossing a first soybean plant or germplasm with a second soybean plant or germplasm, wherein said first soybean plant or germplasm comprises a chromosomal interval selected from the group consisting of:

-   -   1) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 1251375 of SEQ ID NO: 1; or     -   2) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 2515428 of SEQ ID NO: 2.; or     -   3) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 365842 of SEQ ID NO: 3.; or     -   4) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 646429 of SEQ ID NO: 4.; or     -   5) chromosomal interval derived from PI441001, PI441008,         PI446958, PI509501, PI583970, or PI483224 wherein said         chromosomal interval corresponds with nucleotide base 1 to         nucleotide base 750080 of SEQ ID NO: 5; or     -   6) A chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1         cM, 0.5 cM from a SNP marker that associates with increased ASR         resistance in soybean wherein the SNP marker is selected from         the group consisting of any SNP marker displayed in Tables 1-5;         and crossing with a second soybean plant not comprising the         chromosome interval then producing a progeny plant with         increased ASR resistance. Either the first or second soybean         plant or germplasm, or both, may be of a non-naturally occurring         variety of soybean. In some embodiments, the second soybean         plant or germplasm is of an elite variety of soybean. In some         embodiments, the genome of the second soybean plant or germplasm         is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,         95%, 97%, 99% or 100% identical to that of an elite variety of         soybean.

Also provided herein is a method of introgres sing an allele associated with enhanced Disease (e.g. ASR, SCN, SDS, RKN, Phytopthora, etc.) resistance / tolerance into a soybean plant. Such methods for introgressing an allele associated with enhanced Disease (e.g. ASR, SCN, SDS, RKN, Phytopthora, etc.) resistance / tolerance into a soybean plant or germplasm may comprise, consist essentially of or consist of crossing a first soybean plant or germplasm comprising said allele (the donor) wherein said allele is selected from any allele listed in Table 1 or Table 2 or a maker in “close proximity” to a marker listed in Tables 1-5 with a second soybean plant or germplasm that lacks said allele (the recurrent parent) and repeatedly backcrossing progeny comprising said allele with the recurrent parent. Progeny comprising said allele may be identified by detecting, in their genomes, the presence of a marker associated with enhanced Disease (e.g. ASR, SCN, SDS, RKN, Phytopthora, etc.) resistance/tolerance. The marker may be detected in any sample taken from the progeny, including, but not limited to, a portion of said progeny (e.g., a seed chip, a leaf punch disk or a cell from said plant or germplasm) or a nucleotide sequence from said progeny. Such a sample may be taken from the progeny using any present or future method known in the art, including, but not limited to, automated methods of removing a portion of endosperm with a sharp blade, drilling a small hole in the seed and collecting the resultant powder, cutting the seed with a laser and punching a leaf disk. Either the donor or the recurrent parent, or both, may be of a non-naturally occurring variety of soybean. In some embodiments, the recurrent parent is of an elite variety of soybean. In some embodiments, the genome of the recurrent parent is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean.

In some embodiments, the marker used to identify progeny comprising an allele associated with enhanced Disease (e.g. ASR, SCN, SDS, RKN, Phytopthora, etc.) resistance / tolerance may comprise, consist essentially of or consist of one or more marker alleles located within a chromosomal interval selected from the group consisting of:

1) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or

2) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.;

3) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or 4) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.;

5) chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5; or

6) a chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any SNP marker displayed in Tables 1-5 or any closely linked markers in close proximity to said intervals 1)-5).

In some embodiments, the marker may comprise, consist essentially of or consist of marker alleles located in at least two different chromosomal intervals. For example, the marker may comprise one or more alleles located in the chromosomal interval defined by and including any two markers in Table 1, any two markers located in Table 2 any two markers in Table 3 or any two markers in Tables 4 and/or 5.

-   The following are all embodiments contemplated and encompassed     within the invention:     -   1. An elite Glycine max plant having in its genome a chromosomal         interval from a wild

Glycine plant wherein the chromosomal interval comprises any one of SEQ ID NOs: 1-5 or a functional portion thereof that confers ASR resistance in said plant; in some instances the wild Glycine plant is Glycine tomentella and in further instances the wild Glycine plant is selected from any one of plant accessions PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 , wherein said chromosomal interval confers increased Asian soy rust (ASR) resistance as compared to a control plant not comprising said chromosomal interval; Further in a variation of embodiment 1 said elite Glycine max plant is produced by a) performing a non-natural cross between a Glycine max plant and a Glycine tomentella plant wherein “non-natural cross” means a cross between two species that will not produce viable offspring without further intervention (e.g. embryo rescue such as described in Example 3) such as; a) performing embryo rescue as essentially described in Example 3 to create a amphidiploid plant; b) backcros sing the amphidiploid plant of b) with a Glycine max plant for at least 1 backcross generation (preferably BC4) resulting in the generation of an elite Glycine max

-   -   plant having introgressed in its genome said chromosome         interval(s); further the said elite Glycine max plant may have         20 chromosome pairs or could maintain a chromosome pair from         Glycine tomentella and inheriting said intervals to confer ASR         resistance in said elite Glycine max plant.     -   2. The plant of embodiment 1, wherein the chromosomal interval         comprises SEQ ID NOs: 1, 2, 3, 4, 5 or a portion of any thereof         wherein said portion confers ASR resistance to elite Glycine max         plant.     -   3. The plant of embodiments 1-2, wherein the chromosomal         interval comprises a SNP marker associated with increased ASR         resistance wherein said SNP marker corresponds with any one of         the favorable SNP markers as listed in Tables 1-5; or in another         variation a haplotype comprising at least 2 SNP markers         associated with ASR resistance and further wherein the at least         2 SNP markers are selected from any favorable SNP markers as         listed in Tables 1-5.     -   4. The plant of embodiments 1-3, wherein the chromosomal         interval is derived from Glycine tomentella chromosome 5 at an         approximate mapping interval of 0.02-1.19 Mb.     -   5. The plant of embodiments 1-5, wherein the chromosomal         interval corresponds to a position within the wild Glycine         and/or Glycine tomentella genome that comprises SEQ ID NOs: 1-5         or a portion thereof wherein said portion confers increased ASR         resistance in said elite Glycine max plant.     -   6. The plant of embodiments 1-5, wherein the elite Glycine max         plant further shows resistance to any one of the stresses         selected from: diseases (such as powdery mildew, Pythium         ultimum, Phytophthora root rot, leaf spot, blast, brown spot,         root-knot nematode, soybean cyst nematode, soybean vein necrosis         virus, soybean stem canker, soybean sudden death syndrome, leaf         and neck blast, rust, frogeye leaf spot, brown stem rot,         Fusarium, or sheath blight); insect pests (such as whitefly,         aphid, grey field slug, sugarcane borer, green bug, or aphid);         abiotic stress (such as drought tolerance, flooding, high level         of salinity, heavy metal, aluminum, manganese, cadmium, zinc,         UV-B, boron, iron deficiency chlorosis or cold tolerance (i.e.         extreme temperatures)) and further wherein said resistance to         stress is conferred from said chromosomal interval.     -   7. The plant of embodiments 1-6, wherein at least one parental         line of said plant was selected or identified through molecular         marker selection, wherein said parental line is selected or         identified based on a molecular marker located within or closely         associated with said chromosome interval corresponding to any         one of SEQ ID NOs: 1-5.     -   8. The plant of embodiment 7, wherein the molecular marker is a         single nucleotide polymorphism (SNP), a quantitative trait locus         (QTL), a amplified fragment length polymorphism (AFLP), randomly         amplified polymorphic DNA (RAPD), a restriction fragment length         polymorphism (RFLP) or a microsatellite.     -   9. The plant of embodiments 7-8, wherein the molecular marker is         a SNP marker and the molecular marker is any favorable marker as         shown in Tables 1-5.     -   10. The plant of any of embodiments 1-9, wherein the plant is a         agronomically elite Glycine max plant having a commercially         significant yield as well as commercially susceptible: vigor,         seed set, standability or threshability.     -   11. The plant of any of embodiments 1-10, wherein said interval         is introduced into said plant genome by a “non-natural” wide         cross between a Glycine max and Glycine tomentella line followed         by subsequent embryo rescue (e.g. as described in Example 3) and         then resultant plant backcrossed at least once and more         preferably at least four backcrosses (BC4) with Glycine max line         (i.e. in some instances a recurrent Glycine max line) to produce         an elite or agronomically elite Glycine max line.     -   12. The plant of any of embodiments 1-10, wherein said interval         is introduced into said plant genome by transgenic expression or         genome editing of sequences corresponding to and comprising any         one of SEQ ID NOS: 1-5 or a portion thereof wherein said portion         retains ASR resistance when introduced into a susceptible line.     -   13. The plant of embodiment 12, wherein the interval is         introduced by genome editing of a Glycine max genomic region         homologous to, or a ortholog of any of the intervals         corresponding to SEQ ID NOs: 1-5 and further making at least one         genetic edit to said Glycine max genomic region to include at         least 1 allele change corresponding to any favorable allele as         described in any of Tables 1-5 wherein said Glycine max genomic         region did not comprise said allele change before genome edit         and said genome edit confers in plant increased ASR resistance         as compared to a control plant.     -   14. The plant of embodiment 13, wherein the genetic edit is         accomplished through CRISPR, TALEN, meganucleases or through         modification of genomic nucleic acids.     -   15. The plant of embodiments 1-14 wherein the chromosomal         interval comprises any one of or a portion thereof (where said         portion retains ASR resistance) of nucleotide base pair         positions: 1-1251375 of SEQ ID NO: 1; 1-2515428 of SEQ ID NO: 2;         1-365842 of SEQ ID NO: 3; 1-646429 of SEQ ID NO: 4, or 1-750080         of SEQ ID NO: 5.     -   16. A ASR resistant agronomically elite Glycine max plant having         commercially significant yield, wherein said plant comprises an         introgression of a chromosomal interval from a wild Glycine         plant wherein said chromosome interval corresponds to and/or         comprises any one of SEQ ID NOs: 1-5; in some instances said         wild Glycine plant is Glycine tomentella, in further instances         the wild Glycine plant is any one of accessions PI441001,         PI441008, PI446958, PI509501, PI583970, PI483224 or progeny         thereof, wherein the introgression comprises a ASR resistance         conferring QTL linked to at least one marker located on the         chromosome equivalent to Glycine tomentella chromosome 5.     -   17. The ASR resistant elite Glycine max plant of embodiment 16,         wherein said QTL is homozygous.     -   18. The plant of embodiments 16-17, wherein the parental plant         of said ASR resistant agronomically elite Glycine max plant is a         wide cross between Glycine max and Glycine tomentella parental         lines; in one variation the parental line is a amphidiploid         hybrid between Glycine max and Glycine tomentella parental lines         (herein, “amphidiploid hybrid”).     -   19. An agronomically elite Glycine max plant having commercially         significant yield comprising an ASR resistant allele which         confers increased resistance to ASR, and wherein the ASR allele         comprises at least one single nucleotide polymorphism (SNP)         selected from the group of favorable SNPs described in any one         of Tables 1-5 and further wherein said plant comprises in its         genome a chromosomal interval (i.e. such as any one of SEQ ID         NOs: 1-5) from Glycine tomentella or a progeny there of (e.g. a         amphidiploid hybrid).     -   20. An agronomically elite soybean having commercially         significant yield comprising a chromosomal interval from Glycine         tomentella chromosome 5 comprising at least one favorable SNP         marker selected from any one of Tables 1-5; in one variation the         chromosome interval is any one of SEQ ID NOs: 1-5.     -   21. The plant of embodiment 20, wherein said chromosomal         interval from Glycine tomentella chromosome 5 is derived from         any one of plant accessions PI441001, PI441008, PI446958,         PI509501, PI583970, PI483224 or progeny thereof (e.g. such as a         amphidiploid hybrid).     -   22. The plant of embodiments 20-21, wherein the chromosomal         interval comprises SEQ ID

NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5 or a portion thereof wherein said chromosomal interval confers increased ASR resistance in said plant as compared to a control plant not comprising said chromosomal interval.

-   -   23. A plant cell or plant part derived from the plant or seed of         embodiments 1-22; in some instances the plant cell or plant part         cannot be used to regenerate a plant (e.g. thus a plant cell or         plant part unable to be used to regenerate a plant from the         plant or seed of embodiments 1-22).     -   24. A progeny plant or seed from any of the plants of         embodiments 1-22.     -   25. A Glycine max plant of embodiments 1-22, wherein said plant         has 20 chromosome pairs and/or 40 paired chromosomes or in some         instances said plant maintains a chromosomal pair derived from a         wild glycine line.     -   26. A Glycine max plant of embodiments 1-25, wherein there is no         yield drag or negative agronomic effects as compared to a         control plant.     -   27. A method of producing a soybean plant (in some instances a         “amphidiploid hybrid”) having increased resistance to Asian         soybean rust (ASR), the method comprising the steps of:         -   a. crossing a Glycine max plant with a ASR resistant wild             Glycine plant, in some instances a Glycine tomentella plant;         -   b. generating soybean pods from the cross of a);         -   c. isolating embryos from the pods of b) and placing said             embryos onto embryo rescue medium (in some instances the             embryo rescue medium comprises or has a composition             essentially equivalent to: 3.1g B5 basal salt, Gamborg's,             lml B5 vitamins 1000×, 40 g sucrose [C12H220O11], 0.25 g             casein hydrolysate, 0.25 mg BAP, 0.75g MgCl2*6H20, 20 ml             glutamine 25 mg/ml, 0.1 g serine [C3H7NO3], 4ml Asparagine             25 mg/ml, 0.05ml of IBA 1 mg/ml, and 2.0 g Gelzan); or             Murashige and Skoog Medium (MS) or Gamborg's B-5 media             (Bridgen, 1994)) wherein there is no callus induction caused             or initiated in this step c);         -   d. transferring the embryos of c) onto germination medium or             elongation medium (in some instances the germination medium             comprises or has a composition essentially equivalent to:             3.2 g Schenk and Hilderbrandt Basal salt mixture, 1 g             Myo-inositol [C6 H12O6], 5ml Thiamine 1mg/ml, 0.5ml             pyridoxine 1 mg/ml, lOg sucrose [C12H12O11], and 7.5 g             purified agar) or elongation medium comprising or has a             composition essentially equivalent to: 4.3 g MS Basal salt             Mixture [MSP01], 5ml MS iron 200×, 30 g Sucrose [C12H22O11],             1 g MES [C6H13NO4S], 8g purified agar, lml B5 vitamins 100×,             2 ml glutamine 25 mg/ml, 0.50 ml zeatin riboside, trans             isomers 1 mg/ml, 0.1 ml IAA 1 mg/ml, 0.2 ml GA3); and             collecting shoots from said embryos;         -   e. growing the collected shoots of d) on germination or             elongation medium; and         -   f. transferring established shoots of e) to soil, thereby             producing a soybean plant having increased resistance to ASR             (in a preferred instance the shoots are rooted on elongation             or germination medium to form plantlets and subsequently             hardened.)     -   28. The method of embodiment 27, wherein the wild Glycine plant         or Glycine tomentella plant of step a) comprises in its genome a         chromosomal interval corresponding to and defined by (herein, “a         chromosomal defined by” means the interval is the span of         nucleotide bases from the first nucleotide to final nucleotide         of the respective SEQ ID NO:) any one of SEQ ID NOs: 1-5 or a         portion thereof where said portion confers increased ASR         resistance in a plant.     -   29. The method of embodiments 27-28, wherein the Glycine         tomentella plant comprises in its genome an allele associated         with ASR resistance wherein said allele corresponds to any of         the favorable alleles listed in Tables 1-5 or is a allele or SNP         within any one of chromosome intervals comprising any one of SEQ         ID NOs: 1-5 wherein said allele or SNP is associated with or         closely linked to ASR resistance in a plant.     -   30. The method of embodiments 27-29, wherein the wild Glycine or         Glycine tomentella plant is any one of P1441001, P1441008,         P1446958, P1509501, P1583970, P1483224 or progeny thereof (in         some instances the progeny is a amphidiploid hybrid).     -   31. The method of embodiment 30, wherein the progeny plant is a         wide cross between Glycine max and Glycine tomentella parental         lines.     -   32. The method of embodiments 27-31, further comprising the step         of molecular marker selection where an isolated genomic nucleic         acid from any one of: the parent plants of a), the embryo of c)         or the shoot or resultant plant of f) is isolated and analyzed         (e.g. genotyped) for the presence of a allele that associates         with increased ASR resistance and further wherein said allele is         closely linked with the chromosome intervals corresponding to         and defined by SEQ ID NOs: 1-5 (e.g. any of the favorable         alleles as described in any one of Tables 1-5).     -   33. The method of embodiment 32, wherein the allele corresponds         to any of the favorable alleles listed in Tables 1-5.     -   34. The method of embodiments 27-33, wherein the Glycine max         plant of a) has a relative maturity of 3.7 to 4.8. or in other         variations the Glycine max plant may be selected from soybean         maturity groups 000 the X     -   35. The method of embodiments 27-34, wherein the Glycine max         plant of a) is used as a female plant and said wild Glycine or         Glycine tomentella plant is the pollen donor; alternatively in         some instances the Glycine max plant of a) can be uses as the         male pollen donor plant and Wild Glycine or Glycine tomentella         plant is used as a female plant.     -   36. The method of embodiments 27-35, wherein the pods of b) are         treated with a hormone mixture comprising GA3, NAA and Kinetin         (in some embodiments 100 mg GA3, 25mg NAA and 5 mg kinetin /L         and further, in some instances, wherein said hormone treatment         is sprayed on pods daily until harvest).     -   37. The method of embodiments 27-36, wherein the pods are         collected prior to 19 days after pollination.     -   38. The method of embodiments 27-37, wherein the embryos and/or         shoots are treated with a chromosome doubling agent in any one         of steps e)-h) to create amphidiploid plants (or amphidiploid         hybrid) capable of being backcrossed with a domestic annual         Glycine cultivar to produce at least one backcross generation in         some instances a BC4 generation, further wherein the         amphidiploid plant further comprises in its genome a favorable         agronomic trait, such as ASR resistance that was inherited from         the wild Glycine or Glycine tomentella parent; in other         instances the amphidiploid plants are backcrossed with a         recurrent Glycine max parental line followed by embryo rescue         (e.g. as described in embodiments 65-83) to create a BC1 and         repeated multiple times to produce a BC4 generation wherein said         BC4 generation is fertile (i.e. no need for embryo rescue to         generate plants) and capable of producing ASR resistant Glycine         max progeny plants.     -   39. The method of embodiment 38, wherein the chromosome doubling         agent is either colchicine or trifluralin; further contemplated         chromosome doubling agents that may be used in embodiment 38 may         comprise oryzalin.     -   40. The method of embodiments 27-39, wherein the embryos of c)         remains on embryo rescue medium for at least about 20 days at         about 24° C.     -   41. The method of embodiments 27-39, wherein the embryos of d)         remain on germination or elongation medium for at least about 20         days at about 24° C.     -   42. The method of embodiment 41, wherein the embryo rescue         medium is Soy ER1-1 wherein Soy ER1-1 comprises the following:         3.1g B5 basal salt, Gamborg's, 1 ml B5 vitamins 1000×, 40g         sucrose [C12H22O11], 0.25g casein hydrolysate, 0.25ml BAP, 0.75         g MgCl2*6H20, 20 ml glutamine 25 mg/ml, 0.1 g serine [C3H7NO3],         4 ml Asparagine 25 mg/ml and 0.05 ml of IBA 1 mg/ml (herein,         “Soy ER1-1”).     -   43. A method of producing a Glycine max plant having increased         resistance to Asian soybean rust (ASR), the method comprising         the steps of:         -   a. providing a first Glycine max plant comprising in its             genome a chromosomal interval corresponding to any one of             SEQ ID NOs: 1-5 wherein said first Glycine max plant has             increased resistance to ASR;         -   b. crossing the Glycine max plant of a) with a second             Glycine max plant not comprising said chromosomal interval;         -   c. (in some embodiments this step is omitted) selecting a             progeny plant from the cross of b) by isolating a nucleic             acid from said progeny plant and detecting within said             nucleic acid an allele that associates with increased ASR             resistance and further wherein said allele is closely linked             with the chromosome intervals corresponding to SEQ ID NOs:             1-5,         -   d. thereby, producing a Glycine max plant having increased             resistance to ASR.     -   44. The method of embodiment 43, wherein the allele in c)         corresponds to any of the favorable alleles as depicted in any         one of Tables 1-5.     -   45. The method of embodiments 43-44, wherein either first or         second Glycine max plant is an elite Glycine max plant; further         the first or second Glycine max plant could also be an elite         Glycine max plant having commercially significant yield and in         further embodiments be a agronomically elite Glycine max plant.     -   46. The method of embodiments 43-45, wherein the progeny plant         is backcrossed by one or more generations, in some instances at         least four (BC4) backcrosses; in further instances the BC1, BC2,         BC3 generation is followed by embryo rescue as described in         Example 3 or in embodiments 65-82 below.     -   47. The method of embodiments 27-46, wherein the chromosome         interval corresponds to a Glycine tomentella chromosome interval         located on Glycine tomentella chromosome 5 at an approximate         mapping interval of 0.02-1.19 Mb and additionally comprises any         one of SEQ ID NOS: 1-5 or a portion thereof wherein portion         confers ASR resistance or is associated with ASR resistance.     -   48. The method of embodiment 47, wherein the Glycine tomentella         chromosome interval is derived from any one of plant accessions:         P1441001, P1441008, P1446958, P1509501, PI1583970, P1483224 or a         progeny thereof, in some instances the progeny comprises a         amphidiploid hybrid plant.     -   49. The method of embodiment 48, wherein the progeny plant is a         wide cross between Glycine max and Glycine tomentella parental         lines.     -   50. A method of producing a Glycine max plant with increased ASR         resistance, the method comprising the steps of:         -   a) isolating a nucleic acid from a Glycine max plant;         -   b) detecting in the nucleic acid of a) at least one             molecular marker associated with increased ASR wherein said             molecular marker is located within 20 cM, 10 cM, ScM, 1 cM             0.5 cM, or closely linked with a chromosomal interval             corresponding to a genomic region from a wild Glycine plant             or Glycine tomentella plant comprising any one of SEQ ID             NOs: 1-5, or a portion thereof;         -   c) selecting a plant based on the presence of the molecular             marker detected in b) additionally crossing the selected             plant with a second plant (e.g. Glycine max plant) not             comprising said chromosomal interval; and         -   d) producing a Glycine max progeny plant from the plant             of c) identified as having said allele associated with             increased ASR resistance and/or crossed with a second plant.     -   51. The method of embodiment 50, wherein the molecular marker is         closely linked with or corresponds to any one of the favorable         alleles as depicted in Tables 1-5 and/or said molecular marker         is within a chromosomal interval from Glycine tomentella         corresponding to and/or defined by SEQ ID NOs: 1-5.     -   52. A method of identifying and/or selecting a plant (in some         embodiments either a Glycine max or a Glycine tomentella plant)         having a ASR resistance, the method comprising the steps of         -   a. isolating a nucleic acid from a soybean plant or plant             part;         -   b. detecting in the nucleic acid the presence of a molecular             marker that associates with increased ASR resistance wherein             the molecular marker is located within 20 cM, 10 cM, ScM, 1             cM, 0.5 cM of a marker as described in any one of Tables 1-5             or in another embodiment the molecular marker is closely             linked with, in close proximity to, closely associated with             or within a chromosomal interval corresponding to and/or             comprising any one of SEQ ID NOs: 1-5 ; and         -   c. identifying or selecting a soybean plant having increased             ASR resistance on the basis of the molecular marker detected             in b), thereby identifying and/or selecting a plant, having             ASR resistance.     -   53. The method of embodiment 52, wherein the molecular marker         detected in b) consists of any favorable marker as described in         any one of Tables 1-5 or a allele or molecular marker associated         with ASR wherein the allele or molecular marker is located         within a chromosomal interval comprising and defined by any one         of SEQ ID NOs: 1-5.     -   54. The method of embodiments 50-53, wherein the molecular         marker is a single nucleotide polymorphism (SNP), a quantitative         trait locus (QTL), an amplified fragment length polymorphism         (AFLP), randomly amplified polymorphic DNA (RAPD), a restriction         fragment length polymorphism (RFLP) or a microsatellite.     -   55. The method of any one of embodiments 50-54, wherein the         detecting comprises amplifying a marker locus or a portion of         the marker locus and detecting the resulting amplified marker         amplicon (in some embodiments the amplicon comprises a         nucleotide sequence as shown in any one of SEQ ID NOs 1-5;         further, in another embodiment, a primer able to anneal to said         marker locus and amplify said locus allowing for the detection         of the resulting amplified marker amplicon.)     -   56. The method of embodiment 55, wherein the amplifying         comprises: a) admixing an amplification primer or amplification         primer pair with a nucleic acid isolated from the first soybean         plant or germplasm, wherein the primer or primer pair is         complementary or partially complementary to at least a portion         of the marker locus, and is capable of initiating DNA         polymerization by a DNA polymerase using the soybean nucleic         acid as a template; and, b) extending the primer or primer pair         in a DNA polymerization reaction comprising a DNA polymerase and         a template nucleic acid to generate at least one amplicon;         further embodiments, include the primer pair used in said DNA         polymerization reaction and/or a composition comprising said         primer pair.     -   57. The method of embodiments 32-56, wherein the nucleic acid is         selected from DNA or RNA, in some embodiments isolated genomic         DNA and/or RNA.     -   58. The method of embodiments 55-57, wherein the amplifying         comprises employing a polymerase chain reaction (PCR) or ligase         chain reaction (LCR) using a nucleic acid isolated from a         soybean plant or germplasm as a template in the PCR or LCR,         further embodiments wherein said soybean plant is either Glycine         max or Glycine tomentella     -   59. A primer diagnostic for ASR resistance wherein said primer         can be used in a PCR reaction to indicate the presence of an         allele associated with ASR resistance, wherein said allele is         any favorable allele as described in Tables 1-5 and/or said         primer comprises a nucleotide sequence including any of SEQ ID         NOs: 1-5 wherein primer is used in a PCR reaction to generate a         amplicon diagnostic for at least one allele that is associated         with ASR resistance; further a composition comprising said         primer.     -   60. The method of embodiments 27-58, wherein the plant produced         or identified by said methods, further confers increased         resistance to any one of soy cyst nematode, bacterial pustule,         IDC, root knot nematode, frog eye leaf spot, phytopthora, brown         stem rot, nematode, rust, smut, Golovinomyces cichoracearum,         Erysiphe cichoracearum, Blumeria graminis, Podosphaera xanthii,         Sphaerotheca fuliginea, Pythium ultimum, Uncinula necator,         Mycosphaerella pinodes, Magnaporthe grisea, Bipolaris oryzae,         Magnaporthe grisea, Rhizoctonia solani, Phytophthora sojae,         Schizaphis graminum, Bemisia tabaci, Rhopalosiphum maidis,         Deroceras reticulatum, Diatraea saccharalis, Schizaphis graminum         and Myzus persicae; or a combination thereof.     -   61. A plant, seed or plant part produced by the methods of         embodiments 27-58 or 60.     -   62. The plant of claim 61, wherein the plant is an elite Glycine         max plant, in some embodiments the plant is an elite Glycine max         plant having commercially significant yield.     -   63. The plant of embodiment 62, wherein the plant is an         agronomically elite Glycine max plant and in some instances the         agronomically elite Glycine max plant shows commercially         significant yield.     -   64. The plant of embodiments 61-63, wherein said plant displays         no yield drag or negative agronomic effects as compared to a         control and/or check plant; or in other instances has         susceptible commercial performance as compared to a commercial         check.     -   65. A method for producing at least one hybrid between a first         parent plant of a wild perennial Glycine species and a second         parent plant that is a domestic annual Glycine cultivar, wherein         said Glycine cultivar is capable of being backcrossed with a         domestic annual Glycine cultivar to produce at least one plant         of a first backcross generation, or fertile progeny thereof,         said method comprising the steps of:         -   a. providing at least one wild glycine plant (wg) and at             least one domestic annual Glycine parental plant (dg);         -   b. allowing parental plants to flower;         -   c. crossing said wg plant with dg plant (In most embodiments             this cross is a “non-natural cross” thus not able to produce             viable/fertile offspring);         -   d. generating pods from the cross of c);         -   e. isolating embryos from the pods of d) and placing said             embryos onto embryo rescue medium, wherein there is no             callus induction;         -   f. transferring the embryos of e) onto germination medium or             elongation medium and collecting shoots from said embryos;         -   g. growing the collected shoots of f) on germination or             elongation medium; and         -   h. transferring established shoots of e) to soil, thereby             producing a hybrid between a first parent plant of a wild             perennial Glycine species and a second parent plant that is             a domestic annual Glycine; in some embodiments this hybrid             is a amphidiploid hybrid capable of being backcrossed with a             Glycine max plant for at least 1 generation.     -   66. The method of embodiment 65 wherein said wild Glycine line         is selected from the group consisting of G. canescens, G.         argyrea, G. clandestine, G. latrobeana, G. albicans, G.         aphyonota, G. arenaria, G. curvata, G. cyrtoloba, G.         dolichocarpa, G. falcate, G. gracei, G. hirticaulis, G.         lactovirens, G. latifolia, G. microphylla, G. montis-douglas, G.         peratosa, G. pescadrensis, G. pindanica, G. pullenii, G.         rubiginosa, G. stenophita, G. syndetika, and G. tomentella.     -   67. The method of embodiments 65-66, wherein the wild Glycine         parental plant is Glycine tomentella.     -   68. The method of embodiments 65-66, wherein the wild perennial         Glycine carries a desirable agronomic trait such as disease         resistance (e.g. ASR) and/or abiotic stress resistance (e.g.         drought resistance) and/or insect resistance (e.g. Aphid         resistance) and/or higher yield.     -   69. The method of embodiment 68, wherein the desirable trait is         selected from the group consisting of: disease resistance         including but not limited to, resistance to: soy cyst nematode,         bacterial pustule, root knot nematode, frog eye leaf spot,         phytopthora, brown stem rot, nematode, rust, smut, Golovinomyces         cichoracearum, Erysiphe cichoracearum, Blumeria graminis,         Podosphaera xanthii, Sphaerotheca fuliginea, Pythium ultimum,         Uncinula necator, Mycosphaerella pinodes, Magnaporthe grisea,         Bipolaris oryzae, Magnaporthe grisea, Rhizoctonia solani,         Phytophthora sojae, Schizaphis graminum, Bemisia tabaci,         Rhopalosiphum maidis, Deroceras reticulatum, Diatraea         saccharalis, Schizaphis graminum or Myzus persicae; increased         yield, increased resistance or tolerance to iron deficiency         chlorosis, and increased drought or heat tolerance.     -   70. The method of embodiments 65-69, wherein the domestic annual         Glycine is Glycine max.     -   71. The method of embodiments 65-70, wherein the dg plant is         used as a female plant and said wg plant is the pollen donor or         alternatively the dg plant can be used as a pollen donor (i.e.         male line) and wg used as the female line.     -   72. The method of embodiments 65-71, wherein the pods of d) are         treated with a hormone mixture comprising GA3, NAA and Kinetin         (in some embodiments 100 mg GA3, 25 mg NAA and 5 mg kinetin /L         and further, in some instances, wherein said hormone treatment         is sprayed on pods daily until harvest.     -   73. The method of embodiments 65-72, wherein the pods are         collected prior to 19 days after pollination.     -   74. The method of embodiments 65-73, wherein the embryos and/or         shoots are treated with a chromosome doubling agent in any one         of steps e)-h) to create amphidiploid plants capable of being         backcrossed with a domestic annual Glycine cultivar to produce         at least one backcross generation.     -   75. The method of embodiment 74, wherein the chromosome doubling         agent is either colchicine, oryzalin or trifluralin.     -   76. The method of embodiments 65-75, wherein the embryos of e)         remain on embryo rescue medium for at least about 20 days at         about 24° C.     -   77. The method of embodiments 65-76, wherein the embryos of f)         remain on germination or elongation medium for at least about 20         days at about 24° C.     -   78. The method of embodiment 76, wherein the embryo rescue         medium is Soy ER1-1.     -   79. The method of embodiments 65-78, wherein the cross of c)         does not require the emasculation of flowers.     -   80. The method of embodiments 65-79, wherein the cross of c) is         a non-natural cross wherein no viable and/or fertile offspring         would be produced without further intervention such as, for         example, steps d)-h).     -   81. The method of embodiments 65-80, wherein the method further         comprises a step i) wherein the hybrid plant of h) is         backcrossed at least once with a Glycine max plant in most         embodiments the backcross retains a favorable inherited         agronomic trait from said wg, for example, the favorable         agronomic trait could be disease resistance (e.g. ASR) and/or         abiotic stress resistance (e.g. drought resistance) and/or         insect resistance (e.g. Aphid resistance) and/or higher yield;         In further instances the backcross is carried out for four         generations (BC4) resulting in a fertile dg progeny plant         comprising said favorable inherited agronomic trait wherein the         backcross progression follows a wide cross between wg and dg         plant followed by embryo rescue as in embodiment 65 thus         generating a backcrossed plant which is repeated for BC2, BC3,         and in preferred instances BC4 to produce fertile progeny plants         comprising said favorable inherited agronomic trait.     -   82. The method of embodiments 65-81, wherein the method further         comprises step j) wherein the hybrid plant of h) is backcrossed         multiple times and further wherein each back crossed (BC)         generation is selected based on a favorable agronomic trait         derived from said wg line; in some instances each backcross is         followed by (a-h) for four generations (BC4) thus producing         fertile hybrid offspring/progeny plants.     -   83. The method of embodiments 65-82, wherein the method further         comprises step k) counting the number of chromosomes in at least         one BC generation and selecting those that have 40 paired         chromosomes, 20 chromosome pairs or lines not comprising         unpaired chromosomes, or in some instances the plant has more         than 20 chromosome pairs.     -   84. The method of embodiments 65-82, wherein the method further         comprises step k) counting the number of chromosomes in at least         one BC generation and selecting for lines that have no unpaired         chromosomes and carrying these lines forward for further         breeding.     -   85. A amphidiploid plant produced by the method of embodiments         65-85.     -   86. A domestic annual Glycine plant derived from the plant of         embodiment 86.     -   87. A domestic annual Glycine plant of embodiment 87, wherein         the Glycine plant has inherited a desirable agronomic trait from         perennial wild Glycine parent for example, the desirable         agronomic trait could be disease resistance (e.g. ASR) and/or         abiotic stress resistance (e.g. drought resistance) and/or         insect resistance (e.g. Aphid resistance) and/or higher yield.     -   88. The domestic annual Glycine plant of embodiment 88, wherein         the desirable agronomic trait is increased disease resistance to         any one of: soy cyst nematode, bacterial pustule, root knot         nematode, frog eye leaf spot, phytopthora, brown stem rot,         nematode, rust, smut, Golovinomyces cichoracearum, Erysiphe         cichoracearum, Blumeria graminis, Podosphaera xanthii,         Sphaerotheca fuliginea, Pythium ultimum, Uncinula necator,         Mycosphaerella pinodes, Magnaporthe grisea, Bipolaris oryzae,         Magnaporthe grisea, Rhizoctonia solani, Phytophthora sojae,         Schizaphis graminum, Bemisia tabaci, Rhopalosiphum maidis,         Deroceras reticulatum, Diatraea saccharalis, Schizaphis graminum         or Myzus persicae.     -   89. The domestic annual Glycine plant of embodiments 88-89,         wherein the desirable agronomic traits is better field or         commercial performance in regards to any one of the following:         increased yield, lodging, plant height, field emergence,         resistance or tolerance to herbicides, bacteria, fungi, viruses         and nematodes, drought tolerance, heat tolerance, chilling or         freezing tolerance, excessing moisture, salt stress, oxidative         stress, food content and makeup, physical appearance, male         sterility, dry down, standability, prolificacy, sugar         properties, biomass, oil quality or production, protein quality         and overall quality.     -   90. A plant cell, plant part from any of the plants of         embodiments 85-90; in some embodiments said plant cell is         incapable of producing a plant.     -   91. A method of controlling ASR in a field comprising the step         of planting the seed from any of the plants described in         embodiments 1-21; 24-26; 61-64 or 85-89.

Disease resistant Soybean Plants and Germplasms

The present invention provides disease resistant soybean plants and germplasms. As discussed above, the methods of the present invention may be utilized to identify, produce and/or select a disease resistant soybean plant or germplasm (for example a soybean plant resistant or having increased tolerance to Asian Soybean Rust). In addition, to the methods described above, an Disease resistant soybean plant or germplasm may be produced by any method whereby a marker associated with enhanced disease tolerance is introduced into the soybean plant or germplasm, including, but not limited to, transformation, protoplast transformation or fusion, a double haploid technique, embryo rescue, gene editing and/or by any other nucleic acid transfer system.

In some embodiments, the soybean plant or germplasm comprises a non-naturally occurring variety of soybean. In some embodiments, the soybean plant or germplasm is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean.

The disease resistant soybean plant or germplasm may be the progeny of a cross between an elite variety of soybean and a variety of soybean that comprises an allele associated with enhanced Disease tolerance (e.g. ASR) wherein the allele is within a chromosomal interval selected from the group consisting of:

1) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or

2) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.;

3) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or

4) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.;

5) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5.; or

6) a chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM or in close proximity from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any SNP marker displayed in Tables 1-5

The disease resistant soybean plant or germplasm may be the progeny of an introgression wherein the recurrent parent is an elite variety of soybean and the donor comprises an allele associated with enhanced disease tolerance and/or resistance wherein the donor carries a chromosomal interval or a portion thereof comprising any one of SEQ ID NOs: 1-4 and wherein the chromosome interval comprises at least one allele selected respectively from Tables 1-5.

The disease resistant soybean plant or germplasm may be the progeny of a cross between a first elite variety of soybean (e.g., a tester line) and the progeny of a cross between a second elite variety of soybean (e.g., a recurrent parent) and a variety of soybean that comprises an allele associated with enhanced ASR tolerance (e.g., a donor).

The disease resistant soybean plant or germplasm may be the progeny of a cross between a first elite variety of soybean and the progeny of an introgression wherein the recurrent parent is a second elite variety of soybean and the donor comprises an allele associated with enhanced ASR tolerance.

A disease resistant soybean plant and germplasm of the present invention may comprise one or more markers of the present invention (e.g. any marker described in Tables 1-5; or any marker in close proximity to any marker as described in Tables 1-5).

In some embodiments, the disease resistant soybean plant or germplasm may comprise within its genome, a marker associated with enhanced ASR tolerance, wherein said marker is located within a chromosomal interval selected from the group consisting of:

1) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or

2) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.;

3) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or

4) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.;

5) 5) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5.; or

6) a chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM or in close proximity from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any SNP marker displayed in Tables 1-5.

In some embodiments, the disease resistant soybean plant or germplasm may comprise within its genome a marker that comprises, consists essentially of or consists of marker alleles located in at least two different chromosomal intervals. For example, the marker may comprise one or more alleles located in the chromosomal interval defined by and including any combination of two markers in Table 1 and one or more alleles located in the chromosomal interval defined by and including any combination of two markers in Table 2.

Disease Resistant Soybean Seeds

The present invention provides disease resistant soybean seeds. As discussed above, the methods of the present invention may be utilized to identify, produce and/or select a disease resistant soybean seed. In addition to the methods described above, a disease resistant soybean seed may be produced by any method whereby a marker associated with enhanced ASR tolerance is introduced into the soybean seed, including, but not limited to, transformation, protoplast transformation or fusion, a double haploid technique, embryo rescue, genetic editing (e.g. CRISPR or TALEN or MegaNucleases) and/or by any other nucleic acid transfer system.

In some embodiments, the disease resistant soybean seed comprises a non-naturally occurring variety of soybean. In some embodiments, the soybean seed is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 99% or 100% identical to that of an elite variety of soybean.

The disease resistant soybean seed may be produced by a disease resistant soybean plant identified, produced or selected by the methods of the present invention. In some embodiments, the disease resistant soybean seed is produced by a disease resistant soybean or wild glycine plant (e.g. Glycine tomentella) plant comprising any one of chromosomal intervals corresponding to SEQ ID NOs: 1-5.

A disease resistant soybean seed of the present invention may comprise, be selected by or produced by use of one or more markers from Tables 1-5 of the present invention.

In some embodiments, the disease resistant soybean seed may comprise within its genome, a marker associated with enhanced ASR tolerance, wherein said marker is located within a chromosomal interval selected from the group consisting of:

1) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 1251375 of SEQ ID NO: 1; or

2) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 2515428 of SEQ ID NO: 2.;

3) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 365842 of SEQ ID NO: 3.; or

4) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 646429 of SEQ ID NO: 4.;

5) a chromosomal interval derived from PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 wherein said chromosomal interval corresponds with nucleotide base 1 to nucleotide base 750080 of SEQ ID NO: 5.;

6) a chromosomal interval spanning 20 cM, 15 cM, 10 cM, ScM, 1 cM, 0.5 cM or in close proximity from a SNP marker that associates with increased ASR resistance in soybean wherein the SNP marker is selected from the group consisting of any SNP marker displayed in Tables 1-5.

EXAMPLES

The following examples are not intended to be a detailed catalog of all the different ways in which the present invention may be implemented or of all the features that may be added to the present invention. Persons skilled in the art will appreciate that numerous variations and additions to the various embodiments may be made without departing from the present invention. Hence, the following descriptions are intended to illustrate some particular embodiments of the invention, and not to exhaustively specify all permutations, combinations and variations thereof.

Example 1 Identification of ASR Resistant Wild Glycine Lines

Multiple wild glycine (Glycine tomentella) lines were evaluated for ASR resistance against sixteen rust strains collected across a diverse range of environments. The rust data were generated using single pustule derived isolates from USDA-ARS (FL Q09, FL Q12, LABR13, FLQ11) and field populations (FL Q15, FLQ16, RTP1, RTP2, Vero, GA15, UBL, BR south and BR central), the screening was carried out in contained facilities. Of the Glycine tomentella lines screened for ASR resistance, the following Glycine tomentella lines showed broad resistance against all ASR strains tested: PI441001, PI441008, PI446958, PI509501, PI583970, and PI483224.

Each Glycine tomentella line was evaluated over a multiple day course of infection and rated at various time points using a rust rating scale based on groupings modified from Burdon and Speer, TAG, 1984 (see FIG. 6). Each Glycine tomentella accession was screened >2 times with ˜4 plants each time in North & South America using a large diverse panel of rust isolates.

Example 2 Allele Mining & Associations to PI441001, PI441008, PI446958, PI509501, PI583970, or PI483224 ASR Loci

Resistant parent lines (i.e. PI441001, PI441008, PI446958, PI509501, PI583970, and PI483224) were crossed with a susceptible Glycine tomentella line and F1 plants were generated (See Table 5). F1 plants were self-fertilized to generate F2 seed. F2 seed was harvested from the selfed F1 plant. Around 200 F2 seed were sown and leaf tissue from each plant was collected for genotyping studies. Each line was inoculated with Phakopsora pachyrhizi to determine the resistance/susceptible phenotype of each F2 individual. Tissue from 50 resistant F2s and 50 susceptible F2s were combined in separate pools and genomic DNA was prepared from each pool. Illumina sequencing libraries were prepared from DNA for each of the pools and each library was sequenced in two Illumina HiSeq2000 2×100 bp Paired-End (PE) lanes. The average yield per sample was 383 million read pairs, which equals 77 gigabases of sequence per library. The sequencing reads were trimmed to remove bases with PHRED quality scores of <15.

Quality trimmed reads were aligned to the PI441001, PI441008, PI583970, and PI483224 reference genome sequence using GSNAP (WU and NACU 2010) as paired-end fragments. If a pair of reads could not be aligned together, they were treated as singletons for alignment. Reads were used in subsequent analyses if they mapped uniquely to the reference (<2 mismatches every 36 bp and less than 5 bases for every 75 bp as tails).

SNPs were filtered prior to BSA analysis based on read depth, with SNPs having between 40 and 200× read depth being retained. A Chi-square test was used to select SNPs with significantly different read counts between the two alleles in the two pools. An empirical Bayesian approach (LIU et al. 2012) was used to estimate the conditional probability that there is no recombination between each SNP marker and the causal locus in both the resistant pool and in the susceptible pool. The probability of the linkage between the SNP and the causal gene is the geometric mean of these two conditional probabilities. Around 1000 SNPs were found to have possible linkage to the target locus. A subset of these putatively linked SNPs were used to fine map the locus using phenotyped F2 individuals. See references: LIU, S., C.-T. YEH, H. M. TANG, D. NETTLETON AND P. S. SCHNABLE, 2012 Gene Mapping via Bulked Segregant RNA-Seq (BSR-Seq). PLoS ONE 7: e36406 & Wu, T. D., and S. Nacu, 2010 Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.

TABLE 5 Plant Crossings and Study Type Genome F2: Resistant to PI# PI # Size Susceptible Species (male) (female) (Gb) Ratio G. tomentella PI441001 PI441010 2 3:1 G. tomentella PI441001 PI441011 2 3:1 G. tomentella PI441001 PI441010 2 3:1 G. tomentella PI583970 PI441007 2 3:1 G. tomentella PI583970 PI441010 2 3:1 G. tomentella PI583970 PI441011 2 3:1 G. tomentella PI448224 PI441010 2 3:1 G. tomentella PI441008 PI441010 2 7:9

1. PI441001 Data2Bio LLC (Ames, Iowa) Lab Methodology for gBSA-Seq Analysis for Tetraploid Soybean.

-   -   Chromosome discovery for causal loci in the tetraploid soybean         population, PI441001 was carried out using Data2Bio′s Genomic         Bulked Segregant Analysis (gBSA) technology. It was theorized         that ASR resistance is controlled by a single dominant allele.         Four libraries were generated from DNA samples extracted from         two susceptible tissue pools and two resistant tissue pools.         These pools were then sequenced in eight (8) Illumina HiSeq2000         2×100bp Paired-End (PE) lanes. A summary of the reference         genomes used for subsequent analyses, read processing from raw         data to quality trimming, alignment, SNP discovery and SNP         impact are demonstrated in FIGS. 1-5 for population 441001.         After various filtering steps 110,503 informative SNPs were         identified in the PI441001 genome as being significantly         associated with ASR resistance. A Bayesian approach was then         used to calculate trait-associated probabilities. Next, physical         maps of trait-associated SNPs (probability cutoff at 0.01) for         the top contigs were created (FIG. 1). Two scaffolds, 46840 and         49652, were identified in PI441001 (SEQ ID NOs: 1 and 2         respectively). SNPs from these enriched scaffolds were mapped to         the public Glycine max genome. In both populations, most of the         SNPs from the top scaffolds clustered on small portions of Chr05         and Chr08 (see FIG. 4).

2. PI583970 Data2Bio LLC (Ames, Iowa) Lab Methodology for gBSA-Seq Analysis for Tetraploid Soybean

-   -   Chromosome discovery for loci in the tetraploid soybean         population, PI583970 was carried out using Data2Bio′s Genomic         Bulked Segregant Analysis (gBSA) technology. Two libraries were         created from RNA samples extracted from one susceptible tissue         pool and one resistant tissue RNA pool. After various filtering         steps 59,014 informative SNPs were identified in the PI583970         genome that were significantly associated with ASR resistance. A         Bayesian approach was then used to calculate trait-associated         probabilities. Next, a physical map of trait-associated SNPs on         contigs was created. The clustering of these SNPs suggests that         the resistance loci is located in or near scaffold 000819F (see         FIG. 7; Scaffold 001084F is SEQ ID NO: 4). The context sequences         associated with these SNPs were also aligned to the public         Glycine max genome to create a chromosome-level understanding of         the mapping interval. The chromosomal positions of the         trait-associated (ASR resistance) SNPs were then displayed         graphically. Most of the SNPs from scaffold 001084F mapped and         clustered on a small region of Chr05 (see FIG. 8). The data         suggest that the loci responsible for ASR resistance maps within         or near the interval 0.11 to 0.30 Mbp on scaffold 001084F (FIG.         9).

3. PI483224 Data2Bio LLC (Ames, Iowa) Lab Methodology for gBSA-Seq Analysis for Tetraploid Soybean

-   -   Chromosome discovery for causal loci in the tetraploid soybean         population, PI483224 was carried out using Data2Bio′s Genomic         Bulked Segregant Analysis (gBSA) technology. Two libraries were         created from DNA samples extracted from one susceptible tissue         pool and one resistant tissue pool (PI483224). After various         filtering steps 428,263 informative SNPs were identified in the         PI483224 genome to be significantly associated with ASR         resistance. A Bayesian approach was then used to calculate         trait-associated probabilities. Next, a physical map of         trait-associated SNPs on contigs was created. The clustering of         these SNPs indicates that the ASR resistance loci is located on         or near scaffold 002687F (see FIG. 10). The context sequences         associated with these SNPs were also aligned to the public         Glycine max genome to create a chromosome-level understanding of         the mapping interval. The chromosomal positions of the         trait-associated (ASR resistant) SNPs were displayed         graphically. Most of the SNPs from scaffold 002687F mapped to a         small region of Chr05 (See FIG. 11). Data indicates that the ASR         loci may map within or near the interval 0.17 to 0.36 MB on         scaffold 002687F (see FIG. 12 and SEQ ID NO: 3).

Example 3 Embryo Rescue & Introgression of R Gene Intervals into Glycine max Lines

Embryo rescue is performed (as described below) and chemical treatment to induce chromosome doubling is applied in order to generate amphidiploid shoots. If the amphidiploid plants are fertile they will be used to backcross with Glycine max. Backcrossing with Glycine max and subsequent embryo rescue will need to be performed for several generations in order to gradually eliminate the perennial Glycine tomentella chromosomes eventually resulting in ASR resistant Glycine max plant

Wide crosses were carried out using Elite Syngenta soybean (Glycine max) lines (RM 3.7 to 4.8). The elite soybean lines are used as the females (pollen recipients) and multiple accessions of Glycine tomentella are used as the males or pollen donors. Selecting flowers from the Glycine tomentella plant containing anthers at the proper developmental stage is important. New, fully-opened, brightly colored flowers hold anthers with mature pollen. The pollen should appear as loose, yellow dust. These flowers are removed from the Glycine tomentella plant and crossed with the elite Glycine max plant for pollination. Pollen from the Glycine tomentella plants should be used within 30 minutes of flower removal. It is also important to identify and select elite soybean flower buds that are ready for pollination. A soybean flower bud is generally ready when it is larger in size when compared to an immature bud. The sepals of the soybean blossoms are lighter in color and the petals are just beginning to appear. First, use a pair of fine-tipped tweezers to carefully detach the sepals from the flower bud to expose the outer set of petals. Then, gently grasp and remove the petals (5 in total) from the flower exposing the ring of stamens surrounding the pistil. Since the stigma is receptive to pollen 1 day before the anthers begin shedding pollen it is important to recognize the stage development of “female ready, male not ready”. When pollinating soybean flowers at this developmental stage it is not necessary to emasculate the female flower. Locate the stigma on the elite soybean flower. Then using 1 male flower, carefully peel off the petals to expose the anthers and gently dust the pollen grains onto the stigma of the soybean flower. Care should be taken not to damage the stigma at any time during this process. Starting the day after pollination a hormone mixture is sprayed onto the pollinated flower and eventual developing F1 pod 1X every day until harvest. The pollinated flower or pod is saturated with a light mist of the hormone mixture, taking care not to cause the flower/pod to prematurely detach from the plant. The mixture contains 100 mg GA3, 25 mg 1-Naphthaleneacetic acid (NAA) and 5 mg kinetin/L distilled water. Application of these hormones aid in the retention of the developing pod and in increased pod growth. The above described wide cross methodology results in success rates significantly higher than that reported in the literature. Further, no emasculation of female flowers is necessary, which saves time and reduces risk of damage to the stigma.

Harvest: Pods from wide crosses are harvested at approximately 14 to 16 days post pollination. (Harvest dates in the literature suggest 19 to 21 days, however the above method allows for faster harvest time and more robust pods.). Pods are collected and counted according to wide cross combination to determine crossing success. The average crossing success across multiple soybean females and 5 different accessions of Glycine tomentella is approximately 40%. The wide cross pods can contain 1 to 3 seeds but generally 2 seeds are found in each F1 pod. The above described methodology allows for pod harvest at 14 to 16 days after pollination, ˜5 days earlier than described in literature.

Embryo rescue: Harvested pods are collected and brought back to the lab to be sterilized. The pods are first rinsed with 70% EtOH for 2 to 3 minutes and then placed in 10% Clorox bleach for an additional 30 minutes on a platform shaker at approximately 130 RPM. Finally, the pods are rinsed multiple times with sterile water to remove any residual bleach. Embryo isolation can begin immediately following pod sterilization or pods can be stored at 4° C. for up to 24 hours prior to embryo isolation. The sterilized pods are next taken to a laminar flow hood where the embryos can be rescued. Individual pods are placed in a sterile petri dish and opened using a scalpel and forceps. An incision is made along the length of the wide cross pod away from the seed. The pod can then be easily opened to expose the seed. Alternatively, two pair of forceps can be used to separate the pod shell. Carefully remove the seed from the pod and place in a sterile petri dish under a dissection microscope. Very fine forceps are needed to isolate the embryo from the seed. With forceps in one hand, gently hold the side of the seed away from the embryo, with the hilum facing up. Use another pair of forceps in the other hand to remove the seed coat from the side of the seed containing the embryo. Peel off the membrane surrounding the embryo and push the embryo up from its bottom side. Embryos should be past the globular developmental stage and preferably past the early heart developmental stage (middle to late heart stage, cotyledon stage and early maturation stage embryos are desired). Isolated embryos are transferred to embryo rescue medium such as Soy ER1-1 (i.e. 3.1g B5 basal salt, Gamborg's, lml B5 vitamins 1000×, 40 g sucrose [C12H22O11], 0.25g casein hydrolysate, 0.25ml BAP, 0.75g MgCl2*6H20, 20ml glutamine 25mg/ml, 0.1g serine [C3H7NO3], 4 ml Asparagine 25mg/ml and 0.05ml of IBA 1 mg/ml) Murashige and Skoog Medium (MS) and Gamborg's B-5 media (Bridgen, 1994) may also be used as embryo rescue medium. Embryos can be treated to induce chromosome doubling at this time. (See below for chromosome doubling details.) Isolated embryos remain on embryo rescue medium for 21 to 30 days at 24° C. Embryos may remain in the dark for the entire incubation on ER1-1, they also can be incubated in the dark and later completed in the light, or may spend the entire incubation in the light. There is not a callus induction stage in this protocol, shoots are developed directly from the embryos which allows for faster turnaround time, plantlet survival and better quality results. The above described embryo rescue method involves direct shoot regeneration from embryos, rather than regeneration through embryogenesis, thus making plant recovery quicker (shoot recovery in approximately 2-3 months, compared to reported up to 1 year timeline in the literature). Further, the following protocol does not require culture in the dark following transfer to germination medium nor does the above protocol require a transfer to rooting medium.

Chromosome doubling treatments: Either colchicine of trifluralin can be used to induce chromosome doubling. Ideally, late heart stage wide cross embryos (or larger) are chemically treated to induce chromosome doubling at any time from immediately following isolation up to 1 week post isolation. The doubling agent can be mixed in either solid or liquid medium and applied for several hours or up to a few days. Trifluralin is used at a concentration of 10-40uM in either solid or liquid media. Alternatively, colchicine is used at a concentration of 0.4-1 mg/ml in either solid or liquid media. Following chemical treatment, embryos are transferred to fresh embryo rescue medium.

Shoot regeneration: Developing embryos are transferred from rescue medium to germination medium such as Soy ER GSMv2 (i.e. 3.2g Schenk and Hilderbrandt Basal salt mixture, lg Myo-inositol [C6H12O6], 5ml Thiamine 1 mg/ml, 0.5 ml pyridoxine 1 mg/ml, 10 g sucrose [C12H22O11], and 7.5g purified agar) for approximately 3 to 5 weeks in the light at 24° C. Alternatively, developing embryos may be transferred from rescue medium to elongation medium such as Soy E1 0 No TCV (i.e. 4.3g MS Basal salt Mixture [MSP01], 5 ml MS iron 200×, 30g Sucrose [C12H22O11], lg MES [C6H13NO4S], 8g purified agar, lml B5 vitamins 100×, 2ml glutamine 25mg/ml, 0.50 ml zeatin riboside, trans isomers 1 mg/ml, 0.1ml IAA 1 mg/ml, 0.2 ml GA3 5mg/ml, 1.5 ml timentin 100 mg/ml, 0.3ml cefotaxime 250mg/ml, 0.5ml vancomycin 100 mg/ml) Shoots can be kept on medium for approximately 3 to 5 weeks in the light at 24° C. Developing shoots may be transferred from media plates to Phytocons containing either germination or elongation medium for further shoot development. Established shoots having suitable roots are moved to soil.

Ploidy Analysis: Ploidy analysis is conducted using a flow cytometer. Leaf tissue for ploidy analysis is collected from small shoots either in culture or after establishment in soil. Tissue is collected on dry ice and stored at −80° C. until analysis, or collected on wet ice and analyzed the same day. A sample size of 0.5cm² is sufficient. Samples are prepared according to the instructions in the Sysmex kit (Sysmex Inc., Kobe Japan). Each sample set contains an untreated F1 plant (not treated to induce chromosome doubling) as a control.

Example 4 ASR Resistance Trait Introgression

Amphidiploid lines generated from the wide cross (i.e. Glycine tomentella crossed with Glycine max) followed by embryo rescue as described in Example 3 were backcrossed multiple times with a recurrent elite Glycine max lines. It is known in the art that multiple backcrosses are needed to generate fertile hybrid lines, in particular the literature suggests that a BC3 generation is necessary. In this case it was determined that an additional backcrosses are necessary, BC4 in the case of G. tomentella×G. max to generate fertile hybrid plants. Fl hybrid plants produced by the methods as described above were created from wide crosses comprising PI441001, PI441008, PI446958, PI509501, PI583970, and PI483224. F1 plants were next crossed as a female with a male recurrent G. max plant to perform a first backcross (BC1 progeny). BC1 Progeny were further backcrossed for multiple generations (e.g. BC2). BC plants are evaluated for ASR resistance, chromosome numbers and in some cases lines are genotyped through use of molecular markers as described herein to detect the presence of chromosome intervals corresponding to SEQ ID NOs 1-5 or any marker identified in Tables 1-5.

The above examples clearly illustrate the advantages of the invention. Although the present invention has been described with reference to specific details of certain embodiments thereof, it is not intended that such details should be regarded as limitations upon the scope of the invention except as and to the extent that they are included in the accompanying claims.

Throughout this application, various patents, patent publications and non-patent publications are referenced. The disclosures of these patents, patent publications and non-patent publications in their entireties are incorporated by reference herein into this application in order to more fully describe the state of the art to which this invention pertains. 

1. An elite Glycine max plant having in its genome a chromosomal interval from a wild glycine plant, wherein said chromosomal interval confers increased Asian soy rust (ASR) resistance as compared to a control plant not comprising said chromosomal interval.
 2. The plant of claim 1, wherein the chromosomal interval comprises SEQ ID NOs: 1, 2, 3, 4, 5, or a portion of any thereof wherein said portion confers in said plant increased ASR resistance.
 3. The plant of claim 1, wherein the chromosomal interval comprises a SNP marker associated with increased ASR resistance wherein said SNP marker corresponds with any one of the favorable SNP markers as listed in Tables 1-5.
 4. The plant of claim 3, wherein the chromosomal interval is derived from Glycine tomentella chromosome 5 at an approximate mapping interval of 0.02-1.19 Mb.
 5. The plant of claim 5, wherein the chromosomal interval corresponds to a position within the Glycine tomentella genome that comprises any one of SEQ ID NOs: 1-5. 6-9. (canceled)
 10. The plant of claim 1, wherein the plant is a agronomically elite Glycine max plant having a commercially significant yield and/or commercially susceptible vigor, seed set, standability or threshability.
 11. The plant of claim 1, wherein said interval is introduced into said plant genome by a wide cross between a Glycine max and Glycine tomentella line followed by embryo rescue to create amphidiploid hybrid lines capable of being backcrossed with a Glycine max line to create an elite Glycine max plant. 12-15. (canceled)
 16. A ASR resistant agronomically elite Glycine max plant having commercially significant yield, wherein said plant comprises an introgression from a Glycine tomentella accession P1441001, P1441008, P1446958, P1509501, P1583970, P1483224, or progeny thereof, wherein the introgression comprises a ASR resistance conferring QTL linked to at least one marker located on the chromosome equivalent to Glycine max chromosome 5 and wherein said marker is closely linked with or located within a chromosome interval corresponding to and defined by any one of SEQ ID NOS: 1-5.
 17. (canceled)
 18. (canceled)
 19. An agronomically elite Glycine max plant comprising an ASR resistance allele which confers increased resistance to ASR, and wherein the ASR resistance allele comprises at least one single nucleotide polymorphism (SNP) selected from the group of favorable SNPs described in any one of Tables 1-5. 20-22. (canceled)
 23. A plant cell, seed or plant part derived from the plant of claim 1 .
 24. A progeny plant from the plant of claim
 1. 25. (canceled)
 26. (canceled)
 27. A method of producing a Glycine plant having increased resistance to Asian soybean rust (ASR), the method comprising the steps of: a. crossing a Glycine max plant with a ASR resistant Glycine tomentella plant; b. generating soybean pods from the cross of a); c. isolating embryos from the pods of b) and placing said embryos onto embryo rescue medium, wherein there is no callus induction; d. transferring the embryos of c) onto germination medium or elongation medium and collecting shoots from said embryos; e. growing the collected shoots of d) on germination or elongation medium; and f. transferring established shoots of e) to soil, thereby producing a Glycine plant having increased resistance to ASR.
 28. The method of claim 27, wherein the Glycine tomentella plant of step a) comprises in its genome a chromosomal interval corresponding to any one of SEQ ID NOs: 1-5 or a portion thereof.
 29. (canceled)
 30. The method of claim 27, wherein the Glycine tomentella line is any one of P1441001, P1441008, P1446958, P1509501, P1583970, P1483224, or a progeny thereof or a amphidiploid hybrid.
 31. (canceled)
 32. The method of claim 27, further comprising the step of molecular marker selection, wherein an isolated genomic nucleic acid from either the parent plants of a), the embryo of c) or the shoot or resultant plant of f) are analyzed for the presence of a allele that associates with increased ASR resistance and further wherein said allele is closely linked with or located within the chromosome intervals corresponding to SEQ ID NOs: 1-5. 33-35. (canceled)
 36. The method of claim 27, wherein the pods of b ) are treated with a hormone mixture comprising GA3, NAA and Kinetin.
 37. The method of claim 27, wherein the pods are collected prior to 19 days after pollination.
 38. The method of claim 27, wherein the embryos and/or shoots are treated with a chromosome doubling agent in any one of steps e)-h) to create amphidiploid plants capable of being backcrossed with a domestic annual Glycine cultivar to produce at least one backcross generation (BC1).
 39. The method of claim 38, wherein the chromosome doubling agent is either colchicine or trifluralin. 40-42. (canceled)
 43. A method of producing a Glycine max plant having increased resistance to Asian soybean rust (ASR), the method comprising the steps of: a. providing a first Glycine max plant comprising in its genome a chromosomal interval corresponding to any one of SEQ ID NOs: 1-5, wherein said first Glycine max plant has increased resistance to ASR; b. crossing the Glycine max plant of a) with a second Glycine max plant not comprising said chromosomal interval; c. selecting a progeny plant from the cross of b) by isolating a nucleic acid from said progeny plant and detecting within said nucleic acid an allele that associates with increased ASR resistance and further wherein said allele is closely linked with or located within the chromosome intervals corresponding to any one of SEQ ID NOs: 1-5, thereby producing a Glycine max plant having increased resistance to ASR. 44-47. (canceled)
 48. The method of claim 43, wherein the Glycine tomentella chromosome interval is derived from any one of plant accessions: P1441001, P1441008, P1446958, P1509501, P1583970, P1483224, or a progeny thereof.
 49. (canceled)
 50. A method of producing a Glycine max plant with increased ASR resistance, the method comprising the steps of: a) isolating a nucleic acid from a Glycine max plant; b) detecting in the nucleic acid of a) at least one molecular marker associated with increased ASR wherein said molecular marker is located within 20 cM, 10 cM, ScM, 1 cM 0.5 cM, or closely linked with a chromosomal interval corresponding to a genomic region from Glycine tomentella chromosome 5 comprising any one of SEQ ID NOs: 1-5, or a portion thereof, wherein said portion confers to a plant increased ASR resistance; c) selecting a plant based on the presence of the molecular marker detected in b); and d) producing a Glycine max progeny plant from the plant of c) identified as having said allele associated with increased ASR resistance. 51-58. (canceled)
 59. A primer diagnostic for ASR resistance, wherein said primer can be used in a PCR reaction to indicate the presence of an allele associated with ASR resistance, wherein said allele is any favorable allele as described in Tables 1-5. 60-64. (canceled)
 65. A method for producing a hybrid between a first parent plant of a wild perennial Glycine species and a second parent plant that is a domestic annual Glycine cultivar, wherein said hybrid is capable of being backcrossed with a domestic annual Glycine cultivar to produce at least on plant of a first backcross generation, or progeny thereof, said method comprising: a. providing at least one wild perennial Glycine parental plant (wg) and at least one domestic annual Glycine parental plant (dg); b. allowing parent plants to flower; c. crossing said wg plant with dg plant; d. generating pods from the cross of c); e. isolating embryos from the pods of d) and placing said embryos onto embryo rescue medium, wherein there is no callus induction; f. transferring the embryos of e) onto germination medium or elongation medium and collecting shoots from said embryos; g. growing the collected shoots of f) on germination or elongation medium; and h. transferring established shoots of e) to soil, thereby producing a hybrid between a first parent plant of a wild perennial Glycine species and a second parent plant that is a domestic annual Glycine.
 66. The method of claim 65, wherein said wg is selected from the group consisting of G. canescens, G. argyrea, G. clandestine, G. latrobeana, G. albicans, G. aphyonota, G. arenaria, G. curvata, G. cyrtoloba, G. dolichocarpa, G. falcate, G. gracei, G. hirticaulis, G. lactovirens, G. latifolia, G. microphylla, G. montis-douglas, G. peratosa, G. pescadrensis, G. pindanica, G. pullenii, G. rubiginosa, G. stenophita, G. syndetika, and G. tomentella.
 67. The method of claim 66, wherein the wild perennial Glycine parental plant is Glycine tomentella.
 68. The method of claim 67, wherein the wild perennial Glycine carries a desirable agronomic trait.
 69. (canceled)
 70. The method of claim 65, wherein the domestic annual Glycine is Glycine max. 71-84. (canceled)
 85. A amphidiploid plant produced by the method of claim 65-84.
 86. A domestic annual Glycine plant derived from the plant of claim
 85. 87-92. (canceled) 